From 0d90128440fd093084da1e2b8f5d90e45f5b51a1 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 21 Mar 2024 15:36:25 +0100
Subject: [PATCH 01/97] add ChewBBACA

---
 tools/chewbbaca/.shed.yml                     |  15 +
 tools/chewbbaca/AlleleCall.xml                | 161 ++++++
 tools/chewbbaca/CreateSchema.xml              | 119 +++++
 tools/chewbbaca/macros.xml                    |  26 +
 .../GCA_000007265.1_ASM726v1_genomic.fna      | 500 ++++++++++++++++++
 .../GCA_000007265.1_ASM726v1_schema_seed.zip  | Bin 0 -> 31097 bytes
 6 files changed, 821 insertions(+)
 create mode 100644 tools/chewbbaca/.shed.yml
 create mode 100644 tools/chewbbaca/AlleleCall.xml
 create mode 100644 tools/chewbbaca/CreateSchema.xml
 create mode 100644 tools/chewbbaca/macros.xml
 create mode 100644 tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_genomic.fna
 create mode 100644 tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip

diff --git a/tools/chewbbaca/.shed.yml b/tools/chewbbaca/.shed.yml
new file mode 100644
index 00000000000..7c3d125ed42
--- /dev/null
+++ b/tools/chewbbaca/.shed.yml
@@ -0,0 +1,15 @@
+categories: 
+- Variant Analysis
+description: BSR-Based Allele Calling Algorithm
+long_description: chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. chewBBACA performs the schema creation and allele calls on complete or draft genomes.
+homepage_url: https://github.com/B-UMMI/chewBBACA/tree/master
+name: chewbbaca
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for {{ tool_name }}."
+suite:
+  name: "suite_chewbbaca"
+  description: "A suite of Galaxy tools designed to work with the chewbbaca-tools collection."
+  type: repository_suite_definition
diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
new file mode 100644
index 00000000000..01084671bcb
--- /dev/null
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -0,0 +1,161 @@
+<tool id="AlleleCall" name="ChewBBACA AlleleCall" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>Determine the allelic profiles of a set of genomes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir ./input &&
+        mkdir ./schema &&
+        #for $file in $input_file
+        cp $file ./input/${file.element_identifier} &&
+        #end for
+        unzip $input_schema -d ./schema &&
+        chewBBACA.py AlleleCall
+            #if str($advanced.training_file) != 'None'
+                --ptf '$advanced.training_file'
+            #end if            
+            --bsr $blast_score_ratio
+            --l $minimum_length
+            --t $translation_table
+            --st $size_threshold
+            --pm $prodigal_mode
+            --mode $mode
+            --force-continue
+            -i ./input -g ./schema/schema_seed/ -o ./output
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
+        <param format="zip" name="input_schema" type="data" multiple="True" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <section name="advanced" title="Advanced options">
+            <param argument="--training_file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--blast_score_ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
+            <param argument="--minimum_length" type="integer" min="1" value="201" label="Minimum sequence length value"/>
+            <param argument="--translation_table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
+            <param argument="--size_threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+            <param argument="--no-inferred" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Add the sequences of inferred alleles (INF) to the schema" help="Use this parameter if the schema is being accessed by multiple processes/users simultaneously." />
+            <param argument="--prodigal_mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">
+                <option value="single" selected="true">
+                        single
+                    </option>
+                    <option value="meta">
+                        meta
+                    </option>
+            </param>
+            <param argument="--mode" type="select" label="Execution mode" >
+                <option value="1">Only exact matches at DNA level</option>
+                <option value="2">Exact matches at DNA and Protein level </option>
+                <option value="3">Exact matches and minimizer-based clustering to find similar alleles based on BSR+0.1 </option>
+                <option value="4" selected="true">Exact matches and minimizer-based clustering to find similar alleles based on BSR+0.1 </option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="allelecall_results" type="list" label="${tool.name} on ${on_string}: AlleleCall Results">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="./output"/>
+        </collection>
+        <collection name="allelcall_log" type="list" label="${tool.name} on ${on_string}: AlleleCall Logs">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" format="txt" directory="./output"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
+            <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <output_collection name="allelecall_results">
+                <element name="paralogous_loci" ftype="tabular">
+                    <assert_contents>
+                        <has_text_matching expression="Genome.*Loci.*CDS"/>
+                    </assert_contents>
+                </element>
+                <element name="results_alleles" ftype="tabular">
+                    <assert_contents>
+                        <has_text_matching expression="1.*1.*NIPHEM.*NIPH.*1.*1"/>
+                        <has_text_matching expression="GCA_000007265.*1"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+        
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+==========================
+  chewBBACA - AlleleCall
+==========================
+Performs allele calling to determine the allelic profiles of a set of samples in FASTA format. The
+process identifies new alleles, assigns an integer identifier to those alleles and adds them to the
+schema.
+                                                
+  -i, --input-files [INPUT_FILES]               Path to the directory with the genome FASTA files or
+                                                to a file that contains a list of full paths to the
+                                                FASTA files, one per line. (default: None)
+                                                
+  -g, --schema-directory SCHEMA_DIRECTORY       Path to the schema directory. The schema directory
+                                                contains the loci FASTA files and a folder named
+                                                "short" that contains the FASTA files with the loci
+                                                representative alleles. (default: None)
+                                                
+  -o, --output-directory OUTPUT_DIRECTORY       Output directory where the allele calling results
+                                                will be stored (will create a subdirectory named
+                                                "results_<TIMESTAMP>" if the path passed by the user
+                                                already exists). (default: None)
+                                                
+  --ptf, --training-file PTF_PATH               Path to the Prodigal training file. Default is to
+                                                get the training file from the schema's directory
+                                                (default: None)
+                                                
+  --bsr, --blast-score-ratio BLAST_SCORE_RATIO  BLAST Score Ratio value. Sequences with alignments
+                                                with a BSR value equal to or greater than this value
+                                                will be considered as sequences from the same gene.
+                                                (default: None)
+                                                
+  --l, --minimum-length MINIMUM_LENGTH          Minimum sequence length accepted for a coding
+                                                sequence to be included in the schema. (default:
+                                                None)
+                                                
+  --t, --translation-table TRANSLATION_TABLE    Genetic code used to predict genes and to translate
+                                                coding sequences. Must match the genetic code used
+                                                to create the training file. (default: None)
+                                                
+  --st, --size-threshold SIZE_THRESHOLD         CDS size variation threshold. At the default value
+                                                of 0.2, alleles with size that deviates +-20 percent
+                                                from the locus length mode will be classified as
+                                                ASM/ALM (default: None)
+                                                
+  --pm, --prodigal-mode {single,meta}           Prodigal running mode ("single" for finished
+                                                genomes, reasonable quality draft genomes and big
+                                                viruses. "meta" for metagenomes, low quality draft
+                                                genomes, small viruses, and small plasmids).
+                                                (default: single)
+                                                
+  --no-inferred                                 If provided, the process will not add the sequences
+                                                of inferred alleles (INF) to the schema. Allelic
+                                                profiles will still include the allele identifiers
+                                                attributed to the inferred alleles. Use this
+                                                parameter if the schema is being accessed by
+                                                multiple processes/users simultaneously. (default:
+                                                False)
+                                                
+  --mode {1,2,3,4}                              Execution mode (1: only exact matches at DNA level;
+                                                2: exact matches at DNA and Protein level; 3: exact
+                                                matches and minimizer-based clustering to find
+                                                similar alleles based on BSR+0.1; 4: runs the full
+                                                process to find exact matches and similar matches
+                                                based on BSR value, including the determination of
+                                                new representative alleles to add to the schema).
+                                                (default: 4)
+                                                
+
+It is strongly advised to perform allele calling with the default schema parameters to ensure more
+consistent results. Module documentation available at
+https://chewbbaca.readthedocs.io/en/latest/user/modules/AlleleCall.html
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file
diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
new file mode 100644
index 00000000000..6f583e5acfb
--- /dev/null
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -0,0 +1,119 @@
+<tool id="CreateSchema" name="chewBBACA CreateSchema" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>Create a gene-by-gene schema</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir ./input &&
+        #for $file in $input_file
+        cp $file ./input/${file.element_identifier} &&
+        #end for
+        chewBBACA.py CreateSchema 
+            #if str($advanced.training_file) != 'None'
+                --ptf '$advanced.training_file'
+            #end if
+            --bsr $blast_score_ratio
+            --l $minimum_length
+            --t $translation_table
+            --st $size_threshold
+            --pm $prodigal_mode
+            -i ./input -o ./output &&
+        cd output/ &&
+        zip -r schema_seed.zip ./schema_seed
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
+        <section name="advanced" title="Advanced options">
+            <param argument="--training_file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--blast_score_ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
+            <param argument="--minimum_length" type="integer" min="1" value="201" label="Minimum sequence length value"/>
+            <param argument="--translation_table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
+            <param argument="--size_threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+            <param argument="--prodigal_mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">
+                <option value="single" selected="true">
+                        single
+                    </option>
+                    <option value="meta">
+                        meta
+                    </option>
+            </param>
+        </section>
+        <section name="output" title="Output options">
+            <param name="show_cds_invalid" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output invalid CDS file?"/>
+            <param name="show_cds_coord" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output CDS coordinates File?"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="zip" name="schema" from_work_dir="output/schema_seed.zip" label="${tool.name} on ${on_string}: Schema files"/>
+        <data format="txt" name="txt_file" from_work_dir="output/invalid_cds.txt" label="${tool.name} on ${on_string}: invalid CDS">
+            <filter>output['show_cds_invalid']</filter>
+        </data>
+        <data format="tsv" name="tst_file" from_work_dir="output/cds_coordinates.tsv" label="${tool.name} on ${on_string}: CDS coordinates">
+            <filter>output['show_cds_coord']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+        <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
+        <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+============================
+chewBBACA - CreateSchema
+============================
+usage: 
+Create schema from genome assemblies.
+
+positional arguments:
+CreateSchema
+
+options:
+
+-i, --input-files [INPUT_FILES]               Path to the directory that contains the input FASTA
+                                                files. Alternatively, a file with a list of full
+                                                paths to FASTA files, one per line. (default: None)
+                                                
+-o, --output-directory OUTPUT_DIRECTORY       Output directory where the process will store
+                                                intermediate files and create the schema's
+                                                directory. (default: None)
+                                                
+--ptf, --training-file PTF_PATH               Path to the Prodigal training file. (default: None)
+                                                
+--bsr, --blast-score-ratio BLAST_SCORE_RATIO  BLAST Score Ratio value. Sequences with alignments
+                                                with a BSR value equal to or greater than this value
+                                                will be considered as sequences from the same gene.
+                                                (default: 0.6)
+                                                
+--l, --minimum-length MINIMUM_LENGTH          Minimum sequence length value. Coding sequences
+                                                shorter than this value are excluded. (default: 201)
+                                                
+--t, --translation-table TRANSLATION_TABLE    Genetic code used to predict genes and to translate
+                                                coding sequences. (default: 11)
+                                                
+--st, --size-threshold SIZE_THRESHOLD         CDS size variation threshold. Added to the schema's
+                                                config file and used to identify alleles with a
+                                                length value that deviates from the locus length
+                                                mode during the allele calling process. (default:
+                                                0.2)
+                                                
+--pm, --prodigal-mode {single,meta}           Prodigal running mode ("single" for finished
+                                                genomes, reasonable quality draft genomes and big
+                                                viruses. "meta" for metagenomes, low quality draft
+                                                genomes, small viruses, and small plasmids).
+                                                (default: single)
+                                                
+
+It is strongly advised to provide a training file to create a schema. Module documentation available
+at https://chewbbaca.readthedocs.io/en/latest/user/modules/CreateSchema.html
+        ]]>
+    </help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file
diff --git a/tools/chewbbaca/macros.xml b/tools/chewbbaca/macros.xml
new file mode 100644
index 00000000000..ffe84c0c009
--- /dev/null
+++ b/tools/chewbbaca/macros.xml
@@ -0,0 +1,26 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@CHEW_VERSION@">chewBBACA</requirement>
+            <requirement type="package" version="@BLAST_VERSION@">blast</requirement>
+            <requirement type="package" version="@ZIP_VERSION@">zip</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@CHEW_VERSION@">1.15.1</token>
+    <token name="@BLAST_VERSION@">1.15.1</token>
+    <token name="@ZIP_VERSION@">1.15.1</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+            @misc{githubchewBBACA,
+            author = {LastTODO, FirstTODO},
+            year = {TODO},
+            title = {chewBBACA},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/B-UMMI/chewBBACA}
+            </citation>
+        </citations>
+    </xml>
+</macros>
diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_genomic.fna b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_genomic.fna
new file mode 100644
index 00000000000..c6394b7578c
--- /dev/null
+++ b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_genomic.fna
@@ -0,0 +1,500 @@
+>AE009948.1 Streptococcus agalactiae 2603V/R, complete genome
+AATTAACATTGTTGATTTTATTCTTCAACATCTGTGGAAAACTTTATTTTTTTATGGTACAATATAACAATAATTATCCA
+CAAGACAATAAGGAAGAAGCTATGACGGAAAACGAACAACTATTTTGGAATAGAGTACTAGAGCTATCTCGTTCTCAAAT
+AGCACCAGCAGCTTATGAATTTTTTGTTCTAGAGGCTAGACTCCTCAAAATTGAACATCAAACTGCAGTTATTACTTTAG
+ATAACATTGAAATGAAAAAGCTATTCTGGGAACAAAATTTGGGGCCTGTTATCCTAACAGCTGGTTTTGAAATTTTCAAT
+GCTGAAATTACAGCTAACTATGTCTCAAACGATTTACATTTACAAGAAACTAGTTTTTCTAACTACCAGCAATCTAGCAA
+TGAAGTAAATACTTTACCAATTAGAAAAATCGACTCTAACCTTAAAGAGAAATATACTTTTGCTAATTTTGTTCAAGGAG
+ATGAAAATAGATGGGCTGTTTCAGCATCAATTGCTGTAGCTGATAGTCCTGGCACGACTTATAATCCTCTATTTATCTGG
+GGGGGACCTGGTCTAGGAAAGACGCATCTACTAAATGCTATTGGAAATCAAGTCTTAAGAGATAATCCAAACGCGAGGGT
+TTTATACATCACTGCTGAGAATTTTATTAATGAATTTGTCAGTCATATTCGTTTAGATTCGATGGAAGAATTAAAAGAAA
+AGTTTCGCAACTTAGACTTACTCCTGATTGATGATATTCAGTCGCTTGCTAAGAAAACCTTAGGGGGGACCCAAGAGGAG
+TTCTTCAATACTTTCAATGCTTTACATACAAACGATAAACAAATCGTATTGACCAGTGACCGAAATCCAAATCAATTAAA
+TGATCTAGAAGAACGTCTAGTCACGCGCTTTAGTTGGGGACTCCCAGTAAATATCACACCACCTGATTTTGAAACACGAG
+TTGCTATTTTAACCAATAAAATTCAAGAATATCCTTATGATTTTCCTCAAGATACCATTGAATACTTAGCAGGAGAATTT
+GATTCCAACGTACGTGAATTAGAAGGAGCCTTGAAAAATATTAGTCTAGTTGCTGACTTTAAGCATGCTAAAACTATTAC
+AGTAGATATAGCTGCAGAAGCTATCAGAGCACGTAAAAATGATGGTCCTATTGTTACTGTCATTCCTATAGAAGAAATTC
+AAATACAAGTTGGTAAATTCTATGGCGTAACTGTAAAAGAGATAAAAGCAACTAAAAGAACACAAGATATTGTCCTTGCA
+AGACAGGTAGCCATGTACTTAGCTCGTGAGATGACAGATAACAGTCTCCCAAAAATAGGTAAAGAATTTGGGGGACGAGA
+TCACTCAACTGTTCTCCACGCTTATAATAAAATAAAAAATATGGTTGCTCAAGATGACAACTTACGAATTGAGATAGAAA
+CTATCAAAAATAAAATCAGATAGGCTTTGTGGATAAGTATCAGAAAAATACGAGACTTTTCCACAGGTTGTGAACAAGTT
+ATTTTCCTTATGAATATTAAAGTTATAATACTTATTCACAACTTTAACAGGACCTACTATTACTACTAAATTTATACTAA
+TATATAAAGGATATACTATGATTCATTTTTCAATAAATAAAAATTTCTTCTTGCATGCTCTAACGGTAACCAAACGAGCT
+ATTAGTCATAAAAATGCGATTCCAATCCTTTCAACTGTTAAAATAGAAGTGACTAGGGATGCTATCATTTTAACGGGGTC
+AAATGGACAAATTTCAATTGAAAATACTATTCCTGCTTCAAATGAAAATGCAGGTTTACTAGTAACGAATCCAGGCTCTA
+TTTTGTTAGAAGCTGGTTTCTTTATTAATATTATTTCAAGTTTACCAGATGTAACTTTAGAATTTACAGAGATTGAACAA
+CATCAAATTGTTCTTACTAGTGGAAAATCAGAGATTACTTTGAAAGGTAAGGATGTCGATCAATACCCTCGTCTGCAGGA
+AATGACAACAGATACTCCATTAACATTAGAAACTAAACTGTTAAAATCAATTATTAATGAAACTGCTTTTGCTGCTAGCC
+AACAAGAAAGCCGTCCAATCTTAACAGGTGTTCATTTGGTTATCAGTCAAAATAAATACTTTAAGGCTGTTGCGACAGAT
+TCACACCGTATGAGTCAACGCACTTTCCAATTAGAGAAATCGGCTAATAATTTTGATTTGGTTGTTCCAAGTAAATCCCT
+TCGAGAATTTTCGGCTGTTTTTACAGATGATATTGAAACTGTAGAGGTTTTCTTCTCAGATAGTCAAATGTTATTTAGAA
+GTGAAAATATCAGCTTCTATACACGTTTGCTTGAAGGAAACTACCCTGATACTGATCGCCTCCTAACTAATCAGTTTGAA
+ACCGAAATTATCTTTAATACAAATGCTTTACGCCATGCTATGGAACGTGCTTATTTAATTTCGAATGCAACTCAGAACGG
+TACTGTTCGTTTAGAAATTCAAAATGAGACAGTCTCAGCTCATGTAAACTCTCCAGAAGTTGGTAAAGTTAATGAGGAAT
+TGGATACTGTTAGTCTTAAAGGTGATAGTTTAAATATTAGCTTTAATCCAACTTACCTAATTGAATCTTTAAAAGCAGTA
+AAAAGCGAAACAGTTACGATTCGATTTATTTCTCCAGTACGTCCATTTACTTTGACACCTGGTGAAGATACTGAAGATTT
+CATCCAATTAATAACTCCTGTTCGTACTAACTAAATAAGAAAACTACCCAAGTTATTCTTGGGTAGTTTTCTTATTCTAA
+GATATGCTATAATGATGAGTAATATGACTCTATATATAATAGCTAACCCCCATGCTGGTAATAAAAATGCCTCCACTATT
+GTTGGTAAAATTCAGGAGCTTTATCATACTGAAGATATTTCTGTGTTCTATACAGAACAGAAAGATGATGAAAAAAAACA
+AGTCATTAATATACTAAGGTCTTTTAAAGAAAGTGATCATCTAATGATTATAGGAGGAGATGGTACCTTATCAAAAGTAA
+TGACTTATCTCCCCCAACATATTCCGTGCACTTATTATCCTGTTGGTTCGGGAAATGATTTTGCCAGAGCTTTGAAAATT
+CCTAACCTCAAAGAAACCCTTACCGCTATTCAGACAGAAAGATTAAAGGAAATTAATTGCTTTATTTATGATAAAGGGCT
+GATTTTGAATAGTTTAGATTTAGGTTTTGCAGCCTATGTCGTTTGGAAAGCATCTAACTCTAAAATAAAAAATATTTTGA
+ATAGATATCGTCTAGGAAAAATAACTTACATTGTTATAGCTATCAAATCATTATTACATTCTTCTAAAGTACAAGTATTA
+GTGGAAGGAGAGACAGGACAGCAGATAAAACTAAATGACCTTTATTTTTTCGCATTAGCAAATAACACTTATTTTGGAGG
+TGGCATTACTATTTGGCCTAAAGCAAGTGCTTTAACTGCAGAGTTAGATATGGTTTACGCTAAAGGGCATACTTTTCTAA
+AACGATTAAGTATTTTATTATCTTTGGTTTTTAAAAGGCATACTACCTCTAAAAGTATAAAACACCAGACTTTCAAAGCT
+ATGACCGTATATTTTCCTAAAAATAGTTTGATTGAAATAGATGGCGAAATAGTTGAGTTAGATCAGATTAGTTTAAAATG
+TCAAAAAAGGTATTTATATATGTAAGGAGAAAAGATGTATCAAGTTGGATCACTTGTTGAAATGAAAAAACCTCATGCTT
+GTGTAATTAAAGAAACTGGTAAAAAGGCTAATCAATGGAAGGTACTGAGAGTAGGAGCTGATATTAAAATTCAGTGTACT
+AACTGTCAGCATGTGATTATGATGAGTCGTTATGATTTTGAGCGAAAATTAAAAAAAGTACTGCAACCATGAAAGTCCTT
+TTAAACAAATAATTATAGCTATATTTGCAACCAATACTTTCCTAAATAATGCTAGTATGCCGTTGGAAAATTAGCTATTC
+TAATGTTATCGAAAGAAGAAAGGTGGTCATTGACAATGACGAAAGTTGCAGAACAGTTATTTATTTTTCGGTAAGTCATA
+TCAAAATGGGAAAATGGGGATACCACACCAGATTTGGATAATTTAATCAGGTTAGCTGAGATTTTTGACGTGAGCTTAGA
+TGAACATGTTTTAGCTAAAACAAATGAAGTTAAAGTTGAACGTATTTATGAAAATAAACCCCTTGATCTACGAAAATACA
+ATAAAATTTATTGGTTTATTTTTCGAAATATTATTCGATCTCTACTAATTATTTTAGCTATATTAACTTTCTTATAAGCT
+CTAGGTATTCCCTTTGTTTCGGAGTGGATAATTTAAATGAAGGTGAAAGAGTGGCATAATGATAAGCAAATCTGAAATTT
+TCTTCTTATCATACCGCTTTTTCTTCTATTTTTTGATATAATAGTCTTGATTGAAATTTGAATGGAGACTCACTAAATGG
+CTTTAACAGCAGGTATTGTAGGCTTACCAAATGTTGGTAAATCAACTTTATTTAACGCAATTACAAAAGCAGGAGCAGAA
+GCTGCTAATTATCCTTTTGCGACTATTGATCCCAATGTTGGTATGGTAGAAGTACCAGATGAGCGTCTACAAAAATTGAC
+AGAATTGATTACGCCTAAAAAAACAGTTCCGACAACCTTTGAATTTACTGATATTGCAGGTATTGTTAAAGGTGCTTCGA
+AGGGGGAAGGTCTAGGTAATAAATTTTTAGCTAATATTCGTGAAGTGGATGCTATTGTTCATGTGGTACGTGCGTTTGAT
+GATGAAAATGTTATGCGTGAACAAGGTCGTGAGGATGCTTTCGTTGATCCTATAGCAGATATTGATACTATTAATCTTGA
+ATTAATCTTAGCTGATTTAGAGTCAATCAATAAACGTTATGCGCGTGTTGAAAAAATGGCACGAACTCAAAAAGATAAAG
+AATCAGTAGCAGAGTTCAATGTTTTACAAAAGATTAAACCTGTTTTGGAAGATGGGAAATCAGCTCGTACCATTGAGTTT
+ACAGAAGAGGAAGCAAAAGTTGTTAAAGGTCTTTTTTTATTAACAACTAAACCTGTTTTATATGTTGCTAATGTTGATGA
+GGACAAAGTAGCTGATCCTGATGATATCGACTATGTTAATCAAATTCGTGCATTTGCAGAAACAGAGAATGCAGAAGTAG
+TCGTGATTTCTGCTCGAGCTGAAGAAGAAATATCTGAACTTGATGATGAAGATAAGTTAGAATTTTTAGAAGCTATTGGA
+TTAACAGAATCTGGTGTTGATAAATTAACACGAGCTGCTTATCATCTTTTAGGCCTTGGAACTTACTTTACTGCTGGTGA
+AAAAGAGGTTCGCGCTTGGACGTTTAAGCGTGGTATAAAAGCTCCACAAGCTGCTAGTATTATCCATTCAGATTTTGAAA
+GAGGTTTTATTCGTGCAGTAACGATGTCATATGATGACCTTATTCAATATGGATCTGAAAAAGCAGTAAAAGAAGCTGGC
+CGGTTACGTGAAGAAGGAAAAGAGTATATTGTTCAAGATGGCGATATCATGGAATTCCGTTTCAATGTCTAGTAATAAAT
+AATCGATTTGTTAACTTTTAGGTTAAGGATATTGTTAATATCCTTAACCATTTTTGCGTTTTAATGGAGAAGATAATGGT
+AAAAATGATTGTTGGATTAGGAAATCCAGGAAGTAAATATAATGATACAAAACATAATATTGGATTTATGGCTGTTGACA
+GAATTGTAAAAGACCTTGACGTCAACTTTACAGAAGATAAAAATTTTAAAGCAGAGATAGGTAGTGATTTTATCAACGGT
+GAAAAAATTTATTTTATCAAACCGACTACTTTTATGAATAACAGTGGTATTGCTGTAAAAGCCCTGCTTACTTACTACAA
+CATTTCTATTAAGGATATGATTATCATATATGATGATTTAGACATGGAAGTCGGTAAAATACGTTTTCGTCAAAAAGGAT
+CTGCTGGGGGACATAATGGTATCAAGTCTATTATTGCTCATTTAGGTACTCAAGAATTTGATCGTATTAAAGTAGGTATA
+GGACGTCCGAATGGACGTATGACAGTTATTAATCATGTTCTAGGGAAATTTGATAAAAATGATGAAATTATGATATTAAA
+TACCCTTGATAAGGTTGACAATGCTGTCAATTATTATTTACAGACGAATGATTTTCAAAAAACAATGCAGAAATACAACG
+GTTTAAAATGAATATTATAGAATTATTTAGCCAAAATAAAGTGGTGCGGACATGGCACTCTGGATTAGTAACTAATAGTC
+GCCAATTAGTTATGGGGTTTTCAGGAGCAAGTAAAGCTATTGCCATAGCATCAGCCTACGAGAAGTTATCTAAAAAAATT
+ATGGTAGTCACTGCCACTCAAACCGATTCTGATAAATTATCAAGTGATATATCAAGTTTAATTGGAGAAGATAACGTTTA
+TCAATTTTTTGCTGATGACGTTCCTGCAGCAGAGTTTATTTTCTCTTCATTAGATAAATCAATTTCACGACTCAGTGCCC
+TGAGGTTTCTAAAAGATCCAGAAAAAAACGGTGTTTTGATTACTAGTATCAGTGGTTTAAGGTTACTATTACCAAATCCG
+GAAGTTTTCTCGAAAAGTCAATATAAGTTTGAAATCGGTCAAGAATGTTATTTAGATAAATTGTGTAAGAACCTAGTCAA
+TTTAGGTTATCAGAAAGTTTCTCAAGTATTTAGTCCTGGTGAATTTAGCCAAAGAGGAGATATTTTAGATATTTTTGAGA
+TGACACAAGAATATCCTTATCGCTTGGAATTCTTCGGAGATGAAATAGATGGCATCAGGCAGTTTGATATTGACACTCAA
+AAGTCTCTTAAACAATTAGAGTCAGTACAGATTTCGCCAGCAGATGATATTATTTTACAAGATGCAGATTTCGAGCGTGC
+AAAGAAAAAACTTGAGGGCTATCTAGTAACAGCTAGTGAGGTACAACGCACCTATTTGAGCGAGGTTTTATCTACAACTG
+AGAATCATTTTAAGCACTCAGATATTCGTCGTTTTCTAAGTATCTTTTATGAAAAAGAATGGGGAATATTAGACTATATT
+CCTGAGGGAACTCCACTTTTTGTTGATGATTTTCAAAAAATTGTAGATCGAAATGCTAAGTTAGATTTAGAAATAGCTAG
+CCTTCTGACGGAAGATTTACAACAAGGCAAGTCTCATTCTAGTTTGAACTATTTTTCAGATCCTTATAAGCAATTAAGAC
+AATACCAACCAGCAACCTTCTTTTCAAATTTCCACAAAGGATTAGGAAATCTGAAATTTGATAAACTTCATCATTTTACT
+CAATATGGAATGCAAGAATTTTTTAATCAATTTCCATTGTTGGTCGATGAAATCAATCGTTATAAGAAATCTGGAGCGAC
+AGTACTGTTGCAAGTAGATTCTCAAAAAGGTTTAAATCTCCTTCAAGAAAATTTAAAAGAATATGGGTTAGATTTAATCA
+TTTCAGATAAAAACGATATCGTTCAAAAGGAGTCACAACTTATTGTTGGGCATCTTTCAAATGGTTTTTATTTTGCAGAT
+GAGAAAATTGTTCTGATTACTGAACGTGAGATTTATCATAGGCGTGTTAAAAGGAAAATTAGACGCAGTAATATTAGTAA
+TGCAGAACGTCTAAAAGATTATAATGAACTTTCAGTTGGCGATTATGTTGTTCATAATGTTCATGGCGTAGGAAAATTTT
+TAGGTATTGAAACAATTGAGATACAAGGTATTCATCGTGATTATCTGACTATTCAATATCAAAATGCTGATCGTATCTCT
+ATCCCCGTAGAACAAATTGAACTTCTAACAAAATATGTCTCTGCAGATGGCAAAGAGCCTAAAATTAATACGTTAAATGA
+TGGTCGCTTCAAAAAAGCAAAACAGAGAGTTGCAAAGCAAGTAGAAGATATTGCTGATGATTTGTTGAAACTTTATGCAG
+AGCGTAGTCAATTACAAGGATTTGCATTTTCTCCTGACGATAATATGCAAAATGACTTTGATAATGATTTTGCATATGTA
+GAGACAGAGGATCAATTGCGGTCTATAAAAGAAATTAAACAGGATATGGAAGGTAATCGTCCGATGGATCGATTATTGGT
+TGGAGACGTTGGTTTTGGTAAGACAGAGGTTGCTATGCGTGCGGCTTTCAAAGCTGTCAATGACCATAAACAAGTTGTTG
+TTTTAGTCCCAACAACAGTTCTAGCCCAGCAGCATTTTGAAAATTTTAAAGAACGTTTTAGCAATTATCCTGTTACAGTT
+GATGTACTTAGTCGTTTTCGTAGCAAAAAAGAACAAACAGATACACTAAAAAGATTATCTAAGGGCCAAGTTGATATTAT
+TATTGGAACACATCGACTTCTCTCTCAAGATGTTGTATTTTCGGATTTAGGGTTAATAGTTATTGATGAGGAACAGCGAT
+TTGGTGTAAAGCATAAAGAAAAGTTAAAAGAATTAAAAACAAAAGTTGATGTATTAACTTTGACAGCGACCCCAATACCT
+AGAACATTACATATGTCAATGCTTGGCATTAGAGACTTATCAGTCATTGAAACACCTCCAACTAATCGTTATCCTGTGCA
+GACTTACGTTTTGGAGACAAATCCTGGTTTAGTTAGAGAAGCTATTATTCGTGAGATAGACAGAGGAGGACAGGTTTTTT
+ATGTTTACAATAAAGTTGACACTATTGATCAGAAAGTTTCAGAACTTCAGGAGTTAGTACCAGAAGCTAGTATTGGTTTT
+GTTCATGGTCAAATGTCTGAAATTCAATTAGAAAATACATTAATAGACTTTATCAATGGAGATTACGATGTTTTAGTTGC
+AACGACAATAATTGAGACAGGAGTCGATATTTCAAATGTTAATACCCTCTTTGTTGAAAATGCAGATCATATGGGCTTGT
+CAACCCTTTATCAATTAAGAGGCCGTGTGGGTAGAAGTAATCGCATTGCTTATGCTTACCTTATGTACAGACCTGATAAA
+GTTTTAACAGAAATTTCTGAGAAAAGACTAGATGCAATCAAAGGGTTTACAGAATTGGGATCTGGTTTTAAAATAGCGAT
+GCGTGATTTATCTATACGTGGTGCAGGAAATATTTTAGGAGCTTCACAAAGTGGTTTTATTGATTCGGTTGGATTCGAGA
+TGTATTCACAGCTTCTAGAGCAAGCGATTGCCACCAAACAAGGGAAATCATTAATTCGTCAAAAAGGTAATGCTGAATTA
+GCCTTACAAATTGACGCCTATTTACCAGCAGAATATATATCAGATGAGCGCCAAAAAATAGAAATATATAAGCGTATTCG
+TGAATTAGAAACTAGGGCTGATTATGAAGCCTTACAAGATGAGTTAATAGATCGTTTTGGAGAATATCCTGATCAAGTTG
+CATACCTTTTAGAAATAGGACTTTTAAAAGCTTATCTGGACCTTGCCTTTACTGAATTAGTAGAAAGAAAAGGTAATGAA
+ATAAGCATCCTATTTGAAAAAGCATCTTTGAAGTATTTTTTAACTCAAGATTATTTTGAAGCACTATCAAAAACTCAACT
+TAAGGCTAGAATTAGCGAAACAAATGGTAAGATGGAAGTTGTTTTTAATATCAAACATAAGAAAAATTATGAAATTATTG
+AAGAACTTCTAAAATTTGCCGAATGTTTTATCGAGATTAAGTCACGTAAACCAGTAGAAGAATAACTAAGTGAAAAGTTG
+CAAGGAAATTTGGATACTCTTTTAGAAAATGTTTGGTTCAAGAAGAATAGTACGAGCAACATTATGTTTCACGTCAAACA
+TCTCAACTTTTGAAAGACATAAATATTTTTAGAGGTTATTAAAATAGAAGTTTTTTACTTGATATTTGAGAGAATTAAGA
+GAGCTATTAGCTCTCTTTTTGTTACATTATATTGACAAATATTATCAGTTCAGATATTTTTCAAAAAAAATGCTAAAATA
+GTAGAGTTAATTTAGATAGAAGGATGTGATCATCAGTGAGATTAGACAAGTATCTAAAAGTGTCGCGTATCATTAAGCGT
+CGTCCCGTTGCTAAAGAAGTTGCAGACAAAGGACGTGTCAAGGTGAATGGCGTATTAGCAAAGTCATCAACTGACCTAAA
+GCTTAATGACCAAGTTGAAATTCGTTTTGGTAATAAATTGTTGACCGTTAAAGTATTAGAAATGAAAGATAGCACTAAGA
+AAGAAGATGCTATCAAAATGTATGAAATTATTAATGAAACAAGGATAGAAACAGATGAGCAAGCCTAATGTTGTTCAGTT
+AAATAATCAATATATTAACGATGAGAATCTAAAAAAACGTTACGAAGCTGAGGAGTTACGCCGAAAAAATCGTTTAATGG
+GTTGGGTTCTTATTTTTGTCATGCTTTTATTTATTTTACCCACTTATAATTTAGTTAAGAGTTACAGAACTTTACAAGAA
+CGTCGTCAAGAAGTTGTAAAATTAACGAAAGACTATCAGACATTAACTAATAGAACTGAGAACCAGAAGTTGCTAGCAAA
+ACAACTAAAAAATCCAGATTACGTTCAAAAATATGCTCGAGCTAAGTATTATTTCTCTAAGACCGGCGAAATGATTTACC
+CATTACCAGACCTTTTACCAAAATAATTATGAATAATTTAATTGAAACAATAGAACATTTTCTAGCCTACTCGGATGACA
+AACTAGAAGAATTAGCTGATAAGAACTATCAACTTAGGCAAACAATTGTAGAAAAAGAAAAGATTGAGAGCAGAGAAAAG
+TAATGAAGAAAGTTTTAACCTTCTTATTATGTAGCTTATATTTTGTATCAATCCCAGCTATAAGTACCGAGGAGCCATTA
+ACGCTTTCTCAAAATAGACGATACGCCTTAACTCAGACAGTTGTGGATAAGGAAATGTATTTTGATGCTATTCCAGAGAG
+ACCAACTACAAAAATTGAAATAAGCAGTTTTCAAGATGAAGCTTTAACCATAACAGGAGAGACTTTAGTTCCAAATACTT
+TATTGTCGATTGTTTCTCTTACAATTAATTCAAATGGAATTCCAGTATTTACTTTGTCCAATGGACAGTTCATAAAGGCT
+AGTCGTGAAGCTATTTTTAATGATTTAGTTTCTAAGCAGCAATCTGTCTCATTGGATTATTGGTTAAAACCTTCTTTTGT
+GACTTATGAAGCACCTTACACAAATGGTGTTAGTGAAGTTAAAAATAATTTAAAACCTTATTCCAGAGTGCATTTAGTAG
+AACAAGCAGAAACAGAACATGGTATTTATTATAAAACGGACAGTGGTTTTTGGATATCAGTAGAAGATCTATCGGTTGCT
+GATAATCGTATGGCTAAGGTTCAAGAAGTATTATTGGAAAAATATAATAAAGATAAATATGGTATATACATCAAACAATT
+AAATACACAGACAGTAGCTGGTATTAATATTGATAGGTCAATGTACTCTGCAAGTATTGCAAAATTAGCAACACTTTATG
+CTAGCCAAGAGCAAGTAAAATTAGGAAAACTGTCATTGGACAGCAAATTTGAATACAAAGATAATGTTAATCAATTTCCT
+AATAGCTATGATCCAAGTGGTAGTGGGAAATTAGAGAAAAAAGCTGATCATAAATTATATACCGTTAAGGAGTTACTTGA
+AGCAACTGCCAAGGAATCAGATAATGTTGCAACAAATATGCTAGGTTATTATGTCAATAATCAATATGATTCAATGTTTC
+AAACACAAGTAGACACAATTTCTGGTATGCACTGGGATATGAAAAAACGCCAGATTTCTCCACAAGCTGCGGGTAAAATG
+ATGGAAGCAATTTATTATCAAAATGGAGATATTGTTAATTACCTATCAAAGACTGATTTTGATAATACAAGAATCCCTAA
+AAATATACCAGTTAAAGTAGCACATAAAATTGGAGATGCTTATGACTACAAACATGATGCGGCTATTGTTTATGCAGAAC
+AACCTTTTATTATGATTATCTTTACGGATAAATCATCTTACGATGATATCACTAAGATTGCTGACGACGTTTACCAGGTT
+TTAAAATAATATGTATAACACTATTTTGAAAGATACCTTATCCAAAGGGTTATTTACCGCTCATCAGAAAGTTCTAATTG
+CTGTTTCTGGTGGCATTGATTCAATAAATTTGTTGCAATTTTTATACCAGTATCAAAAAGAGTTATCGATTAGTATTGGT
+ATTGCACACATAAATCATGGACAGCGAAAAGAATCAGAAAAAGAAGAAGAATATATCAGACAGTGGGGACAGATACATGA
+TGTCCCTGTCTTTATCTCTTATTTTCAAGGAATATTTTCAGAAGATAGAGCACGTAACCATCGCTACAATTTTTTTTCAA
+AAGTTATGCGTGAAGAAGGTTACACGGCTTTAGTAACAGCTCACCATGCTGATGATCAAGCTGAAACTGTATTTATGAGA
+ATTTTAAGAGGAAGCAGGCTACGCTATTTATCAGGGATTAAGCAAGTGAGTGCTTTTGCAAACGGTCAATTGATTAGACC
+ATTTCTTCCATATAAAAAGGAGTTATTACCAAATATTTTTCATTTTGAAGATGCTAGCAACGCTTCGTCTGATTATTTAA
+GAAATCGAATAAGAAACGTCTACTTTCCTGCTTTGGAAAGAGAAAATAATCAATTGAAAGATTCTCTCATAACTCTCTCT
+GAGGAAACAGAGTGTTTATTCACGGCTTTAACAGACCTAACAAGGAGCATCGAAGTAACAAACTGCTATGATTTTTTAAG
+GCAAACTCATTCTGTCCAAGAATTTTTATTGCAAGATTACATTAGCAAATTTCCAGATTTACAAGTGAGTAAAGAACAGT
+TCAGAGTAATATTAAAATTGATTAGAACTAAAGCCAATATTGACTATACTATTAAATCGGGCTATTTTCTTCATAAGGAT
+TACGAGAGTTTTCATATTACAAAAATCCATCCTAAGACGGATAGTTTTAAGGTTGAAAAAAGATTAGAATTGCATAATAT
+ACAAATATTCTCACAATATTTATTTTCCTATGGAAAATTCATTTCTCAAGCAGACATTACTATTCCTATTTATGATACTT
+CTCCGATTATTTTAAGAAGAAGAAAAGAAGGGGATAGGATATTTTTAGGAAATCACACTAAAAAAATTCGCCGTCTATTT
+ATTGATGAGAAAATAACTCTAAAAGAGAGAGAAGAAGCTGTTATTGGGGAGCAAAATAAAGAGTTGATATTTGTGATTGT
+TGCAGGTAGAACATATTTGAGAAAACCTTCTGAACATGATATAATGAAGGGCAAACTTTATATTGAAAATTTAGAAAAAA
+GGTGACATCATGCTTGAAAATGATATAAAAAAAGTTTTATATTCAGAAGAAGATATTATTCTGAAAACGAAAGAATTAGG
+AGCTAAATTAACTGCAGATTATGCAGGTAAGAATCCATTATTAGTAGGTGTATTAAAGGGGTCAGTGCCTTTTATGGCTG
+AGCTATTAAAGCATATTGATACACATGTTGAAATTGATTTTATGGTTGTTTCAAGCTATCATGGTGGTACAACTAGTAGT
+GGAGAAGTTAAAATTTTAAAAGATGTTGATACTAACATTGAAGGAAGAGATGTAATCTTTATTGAAGACATCATTGATAC
+TGGACGTACATTAAAATACCTTCGAGATATGTTTAAGTATCGCCAAGCTAACTCTGTCAAAGTTGCAACCCTTTTTGATA
+AGCCAGAAGGGCGATTGGTAGATATTGATGCTGATTACGTTTGTTACGATATCCCAAATGAATTTATTGTGGGATTCGGT
+TTAGACTATGCTGAAAACTATCGTAACTTACCTTATGTTGGTGTGTTAAAAGAAGAAATTTACTCAAAATAGAAAAAAGG
+TACTCTCTTAAACTATGAAAAATAATAAAAATAATGGTTTTCTGAAAAATTCCTTTATTTACATATTATTGATTATTGCG
+GTTATTACAACCTTTCAATACTATTTAAAAGGAACTAGCTCTCAAAACCAGCAAATTTCTTATACAAAACTTGTTAAACA
+ATTAAAAGCTGGAGAAATTAAGTCTATCTCATACCAGCCAAGTGGTGGTGTTGTTGAAGTTAGTGGGACATATAAGAAAG
+CCAAAACAATTAAATCAGCTAATAGTTTTACTTTTTTAGGTGGTAGTGTTGCTACTAAAGTTACAGGATTTAATTCTGTT
+ATACTACCAAATGACTCTTCAATAAAATCTCTTGTTAGCGCTGCTGAAGAAAATAACACTAATATTCAGGTCAAACATGA
+AAGTTCAAGTGGGACATGGATTTCTTATATTGCCAGTTTTTTACCTTTAGTTATCATGATTGGTTTCTTCATGATGATGA
+TGAACCAAGGCGGTGGCGGTGGCGCTCGTGGTGCCATGAGCTTTGGTAAAAATAAAGCAAGATCATCTAGTAAAGATGAG
+GTTAAAGTTCGATTTTCGGATGTTGCTGGAGCAGAGGAAGAAAAGCAAGAATTAATAGAAGTCGTTGACTTCCTTAAAGA
+TCCTAAACGATATAAATCTCTAGGTGCCCGAATTCCAGCAGGGGTTCTATTAGAAGGACCTCCAGGGACAGGTAAAACCC
+TATTAGCAAAAGCTGTTGCCGGTGAAGCAGGGGTTCCATTCTTTAGTATTTCCGGTTCAGATTTTGTTGAAATGTTTGTC
+GGTGTTGGAGCTAGTCGAGTACGCTCTTTGTTTGAAGATGCTAAAAAAGCTGAACGTGCTATTATTTTCATTGATGAAAT
+TGATGCTGTTGGACGTCGACGTGGAGCTGGTATGGGTGGCGGAAACGATGAACGTGAACAAACGCTCAACCAACTTTTAA
+TTGAAATGGATGGTTTTGAAGGAAACGAAAGTATTATCGTTATCGCTGCTACCAACCGTAGTGATGTGTTAGATCCCGCA
+TTACTGCGTCCAGGACGTTTTGATAGAAAAGTTCTAGTTGGACAACCTGATGTAAAAGGTCGTGAAGCAATTCTGAGAGT
+ACATGCTAAAAATAAACCATTAGCAGATAATGTTGACTTAAAAGTAGTAGCTCAACAAACCCCAGGATTTGTTGGTGCTG
+ATTTGGAGAATGTTCTCAATGAAGCTGCTTTAGTTGCTGCGCGACGAAATAAAAAAGTTATTGATGCTTCAGATATTGAT
+GAAGCAGAAGACCGTGTAATTGCTGGTCCTTCTAAAAAAGATCGTACTATTTCTGAAAGAGAAAGAGCTATGGTTGCTTA
+CCATGAAGCTGGGCACACAATTGTCGGTTTGATTCTTTCAAATGCGCGAGTTGTTCATAAAGTTACTATCGTACCACGTG
+GTCGTGCAGGTGGATATATGATTGCTTTACCTAAAGAAGATCAAATGCTTCTTTCAAAAGATGATATGAAAGAGCAATTA
+GCAGGTCTTATGGGAGGACGTGTAGCGGAAGAAATTATTTTCAACGCTCAGACAACAGGTGCCTCAAATGACTTCGAACA
+AGCCACTGCTATGGCCCGCGCTATGGTAACTGAATATGGTATGAGCGAGAAACTTGGACCAGTTCAATACGAAGGCAACC
+ACGCAATGATGGCTGGTCAAATGTCACCTGAAAAATCATATTCTGCTCAAACTGCACAACTTATTGATGATGAAGTTCGT
+CACCTTCTTAATGAAGCACGTAATAAGGCAGCTGATATTATCAACGAAAACCGTGATACTCATAAATTAATTGCAGAAGC
+CCTCTTAAAATATGAGACTCTTGATGCTGCTCAGATTAAATCGATTTTTGAGACAGGTAAAATGCCTGAGACAGAAAATG
+ATGAAGATAAAGCAAGAGCGTTATCATACGATGAAATCAAAGAAAAAATGCAAGAAGAAGATAAAAAATAAGTCATCATA
+TATTTTTAAAGAACTTTATAAATTTCAAATACCCTTCAAATTTAGATAAAATTTGAAGGGTATTTTTTATGAAGATGAAG
+TTTAAATTTGTGAATTAAGAAGATGAAATATGAACATGACAACGGTAAAAATGCTATCCATTCAACAAGTATAGAAGGTT
+AGTTACTATAAATAATATTAACTTTTTAAAAATAAAAGAAAAAATGCAAAAATAGTATTGACAGGAAGTAGAAATATTTA
+GTATAATGAATAAGTTGTCTCGAGAGAGCAGCTTCTAGTAACGCGTAGTTAACAACTTAAAAAAAAGTAGTTGACAAAGC
+AGAATAAGTTTGCTAGAATATAGAAGTTGTCTCAAGAGAGGCAAAGACCTTTGAAAACTGAACAAGACGAACGAATGTGC
+AGGGTGGATTTACATTGTAAATCCGTCAATGACAAAAAAACAATAAATCTGTCAGCGAGACAGAAAAGAGCAAAGCTCAA
+ACTTTTAATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTAGAACGCTGAGGTTT
+GGTGTTTACACTAGACTGATGAGTTGCGAACGGGTGAGTAACGCGTAGGTAACCTGCCTCATAGCGGGGGATAACTATTG
+GAAACGATAGCTAATACCGCATAAGAGTAATTAACACATGTTAGTTATTTAAAAGGAGCAATTGCTTCACTGTGAGATGG
+ACCTGCGTTGTATTAGCTAGTTGGTGAGGTAAAGGCTCACCAAGGCGACGATACATAGCCGACCTGAGAGGGTGATCGGC
+CACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGGAAGTCTGACC
+GAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGAGAAGAACGTTGGTAGGAGTGGAAAA
+TCTACCAAGTGACGGTAACTAACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCG
+TTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTA
+CGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGG
+AGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAG
+ATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAGGTGTTAGGCCCTTTCCGGGGCTTAGTGCCGCAGCTAACGCAT
+TAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCAT
+GTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTTCTGACCGGCCTAGAGATAGGCTTTCTCTT
+CGGAGCAGAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCA
+ACCCCTATTGTTAGTTGCCATCATTAAGTTGGGCACTCTAGCGAGACTGCCGGTAATAAACCGGAGGAAGGTGGGGATGA
+CGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGTTGGTACAACGAGTCGCAAGCCGGTGACG
+GCAAGCTAATCTCTTAAAGCCAATCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGTCGGAATCGCTAGTAAT
+CGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCC
+GAAGTCGGTGAGGTAACCTTTTAGGAGCCAGCCGCCTAAGGTGGGATAGATGATTGGGGTGAAGTCGTAACAAGGTAGCC
+GTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGATAAGGAAACCTGCCATTTGCGTCTTGTTTAGTTTTGAGAGG
+TCTTGTGGGGCCTTAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAGGCTCCAT
+TGAATCGAAAGGTTCAAATTGTTCATTGAAAATTGAATATCTATATCAAATTCCACGATCTAGAAATAGATTGTAGAAAG
+TAACAAGAAAATAAACCGAAAACGCTGTGAATATTTAATGAGTTTTCTAGTTTTAAAGAAACTAGGTTAATAAGGTTAAG
+TTAATAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGAAGAAGGACGTGACTAACGACGAAATGCTTTGGGGAGCT
+GTAAGTAAGCGCTGATCCAGAGATGTCCGAATGGGGGAACCCACTAGTTAATGACTAGTATCCATATCTGTTAAGGATAT
+GAGAAGGAAGACGCAGTGAACTGAAACATCTAAGTAGCTGCAGGAAGAGAAAGCAAAAGCGATTGCCTTAGTAGCGGCGA
+GCGAAACGGCAGGAGGGCAAACCGAAGTGTTTACACTTCGGGGTTGTAGGACTGCGATATAGGATTAATCATTATAGAAG
+AATTACCTGGGAAGGTAAGCCAAAGAGAGTAACAGCCTCGTATTTAAAATGATAGATTAACCTTAGCAGTATCCTGAGTA
+CGGCGAGACACGCGAAATCTCGTCGGAATCTGGGAGGACCATCTCCCAACCCTAAATACTCTCTAGTGACCGATAGTGAA
+CCAGTACCGTGAGGGAAAGGTGAAAAGCACCCCGGGAGGGGAGTGAAATAGAACCTGAAACCGTGTGCCTACAACAAGTT
+CGAGCCCGTTAATGGGTGAGAGCGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATATGATGCGAGGTTAAGTTGAAGA
+GACGGAGCCGTAGGGAAACCGAGTCTTAATAGGGCGTCATAGTATCATGTTGTAGACCCGAAACCATGTGACCTACCCAT
+GAGCAGGTTGAAGGTGAGGTAAAACTCACTGGAGGACCGAACCAGGGCACGTTGAAAAGTGCTTGGATGACTTGTGGGTA
+GCGGAGAAATTCCAAACGAACTTGGAGATAGCTGGTTCTCTCCGAAATAGCTTTAGGGCTAGCGTCGATGTTAAGTCTCT
+TGGAGGTAGAGCACTGTTTGGGTGAGGGGTCCATCCCGGATTACCAATCTCAGATAAACTCCGAATGCCAACGAGATATA
+ATCGGCAGTCAGACTGCGAGTGCTAAGATCCGTAGTCGAAAGGGAAACAGCCCAGACCACCAGCTAAGGTCCCAAAATAT
+ATGTTAAGTGGAAAAGGATGTGGGGTTGCACAGACAACTAGGATGTTAGCTTAGAAGCAGCTATTCATTCAAAGAGTGCG
+TAATAGCTCACTAGTCGAGTGACCCTGCGCCGAAAATGTACCGGGGCTAAAACATATTACCGAAGCTGTGGATGACACAA
+AAGTGTCATGGTAGGAGAGCGTTCTATGTGTGAAGAAGGTGTACCGTGAGGAGCGCTGGAACGCATAGAAGTGAGAATGC
+CGGTATGAGTAGCGCAAGACAGGTGAGAATCCTGTCCACCGTAAGACTAAGGTTTCCAGGGGAAGGCTCGTCCGCCCTGG
+GTTAGTCGGGACCTAAGGAGAGACCGAAAGGTGTATCCGATGGACAACAGGTTGATATTCCTGTACTAGAGTATATAGTG
+ATGGAGGGACGCAGTAGGCTAACTAAACCAGACGATTGGAAGTGTCTGGTCAAACAGTGAGGTGTGATATGAGTCAAATG
+CTTATATCTTTAACATTGAGCTGTGACGAGGAGCGAAGTTTAGTAGCGAAGTTAGTGATGTCACACTGCCAAGAAAAGCT
+TCTAGCGATACATATACTCTACCCGTACCGCAAACCGACACAGGTAGTCGAGGCGAGTAGCCTCAGGTGAGCGAGAGAAC
+TCTCGTTAAGGAACTCGGCAAAATGGCCCCGTAACTTCGGGAGAAGGGGCGCTGATTTTAGATCAGCCGCAGTGAATAGG
+CCCAAGCAACTGTTTATCAAAAACACAGCTCTCTGCTAAATCGTAAGATGATGTATAGGGGGTGACGCCTGCCCGGTGCT
+GGAAGGTTAAGAGGAGTGCTTAGCGTAAGCGAAGGTATGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTC
+CTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAATGATTTGGGCACTGTCTCAACGAGAG
+ACTCGGTGAAATTTTAGTACCTGTGAAGATGCAGGTTACCCGCGACAGGACGGAAAGACCCCATGGAGCTTTACTGCAGT
+TTGATATTGAGTATCTGTACCACATGTACAGGATAGGTAGGAGCCTATGATAACGGGACGCCAGTTTCGTTTGAGGCGTT
+GTTGGGATACTACCCTTGTGTTATGGCTACTCTAACCCAGATAGGCAATCCCTATCGGAGACAGTGTCTGACGGGCAGTT
+TGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGACTGGTTGGAAATCAGTCGTAGAGT
+GTAAAGGTATAAGGGAGCTTGACTGCGAGAGCTACAACTCGAGCAGGGACGAAAGTCGGGCTTAGTGATCCGGTGGTTCC
+GTATGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCTGGGGATAACAGGCTTATCTCCCCCAAGAGTTCACATCGACG
+GGGAGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTA
+AAGCGGCACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGTAGGAAATTTGAGAGGA
+TCTGCTCCTAGTACGAGAGGACCAGAGTGGACTTACCGCTGGTGTACCAGTTGTCTTGCCAAAGGCATCGCTGGGTAGCT
+ATGTAGGGAAGGGATAAGCGCTGAAAGCATCTAAGTGCGAAGCCCACCTCAAGATGAGATTTCCCATGATTTTATATCAG
+TAAGAGCCCTGAGAGATGATCAGGTAGATAGGTTAGGAGTGTAATTGTGGTGACACATTTAGCGGACTAATACTAATAGC
+TCGAGGACTTATCCAAAAAGAGATATTGACAACGTTACGGTTTCTTGTTAGACTATAGATATTCAATTTTGAGTGAATAA
+GGCTCAATAGTTAAGTGATAATTGCCTAGGAGATACACCTGTTCTCATGCCGAACACAGAAGTTAAGCCCTAGAACGCCG
+GAAGTAGTTGGGGGTTGCCCCCTGTGAGATAAGGTAGTCGCTTAGCAAAGGGAGTTTAGCTCAGCTGGGAGAGCATCTGC
+CTTACAAGCAGAGGGTCAGCGGTTCGATCCCGTTAACTCCCATAGGTCCCGTAGTGTAGCGGTTATCACGTCGCCCTGTC
+ACGGCGAAGATCGCGGGTTCGATTCCCGTCGGGACCGTAGACTCGTTAGCTCAGTTGGTAGAGCAATTGACTTTTAATCA
+ATGGGTCACTGGTTCGAGCCCAGTACGGGTCATTTAGAAATGCGGGTGTGGCGGAATTGGCAGACGCACCAGATTTAGGA
+TCTGGCGCTTAACGGCGTGGGGGTTCAAGTCCCTTCACCCGCATTAGTAGATTGCCGGCTTAGCTCAGTTGGTAGAGCAT
+CTGATTTGTAATCAGAGGGTCGCGTGTTCAAGTCATGTAGCCGGCATTACAATTTTATAGGATAAATAGTGTCTTTAGTG
+CGAACGTAGTTCAGTGGTAGAACATCACCTTGCCAAGGTGAGGGTCGCGGGTTCGAACCCCGTCGTTCGCTTGTTAGAGG
+CCGGGGTGGCGGAACTGGCAGACGCACAGGACTTAAAATCCTGCGATGGTAAACATCGTACCGGTTCGATTCCGGTCCTC
+GGCATATAATATTTAGCACCCTTAGCTCAACTGGATAGAGTACCTGACTACGAATCAGGCGGTTAGAGGTTCGACTCCTC
+TAGGGTGCATATTTTTCGGGAAGTAGCTCAGCTTGGTAGAGTACTTGGTTTGGGACCAAGGTGTCGCAGGTTCGAATCCT
+GTCTTCCCGATGGATATATTTTTATGATATATCATTAGACCTTTGAAAACTGAACAAGACGAACGAATGTGCAGGGTGGA
+TTTACATTGTAAATCCGTCAATGACAAAAAACAATAAATCTGTCAGCGAGACAGAAAAGAGCAAAGCTCAAACTTTTAAT
+GAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTAGAACGCTGAGGTTTGGTGTTTAC
+ACTAGACTGATGAGTTGCGAACGGGTGAGTAACGCGTAGGTAACCTGCCTCATAGCGGGGGATAACTATTGGAAACGATA
+GCTAATACCGCATAAGAGTAATTAACACATGTTAGTTATTTAAAAGGAGCAATTGCTTCACTGTGAGATGGACCTGCGTT
+GTATTAGCTAGTTGGTGAGGTAAAGGCTCACCAAGGCGACGATACATAGCCGACCTGAGAGGGTGATCGGCCACACTGGG
+ACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGGAAGTCTGACCGAGCAACGC
+CGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGAGAAGAACGTTGGTAGGAGTGGAAAATCTACCAAG
+TGACGGTAACTAACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGA
+TTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGA
+AACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
+GGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGG
+TAGTCCACGCCGTAAACGATGAGTGCTAGGTGTTAGGCCCTTTCCGGGGCTTAGTGCCGCAGCTAACGCATTAAGCACTC
+CGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAA
+TTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTTCTGACCGGCCTAGAGATAGGCTTTCTCTTCGGAGCAGA
+AGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATT
+GTTAGTTGCCATCATTAAGTTGGGCACTCTAGCGAGACTGCCGGTAATAAACCGGAGGAAGGTGGGGATGACGTCAAATC
+ATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGTTGGTACAACGAGTCGCAAGCCGGTGACGGCAAGCTAA
+TCTCTTAAAGCCAATCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGTCGGAATCGCTAGTAATCGCGGATCA
+GCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGT
+GAGGTAACCTTTTAGGAGCCAGCCGCCTAAGGTGGGATAGATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAA
+GGTGCGGCTGGATCACCTCCTTTCTAAGGATAAGGAAACCTGCCATTTGCGTCTTGTTTAGTTTTGAGAGGTCTTGTGGG
+GCCTTAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAGGCTCCATTGAATCGAA
+AGGTTCAAATTGTTCATTGAAAATTGAATATCTATATCAAATTCCACGATCTAGAAATAGATTGTAGAAAGTAACAAGAA
+AATAAACCGAAAACGCTGTGAATATTTAATGAGTTTTCTAGTTTTAAAGAAACTAGGTTAATAAGGTTAAGTTAATAAGG
+GCGCACGGTGGATGCCTTGGCACTAGAAGCCGAAGAAGGACGTGACTAACGACGAAATGCTTTGGGGAGCTGTAAGTAAG
+CGCTGATCCAGAGATGTCCGAATGGGGGAACCCACTAGTTAATGACTAGTATCCATATCTGTTAAGGATATGAGAAGGAA
+GACGCAGTGAACTGAAACATCTAAGTAGCTGCAGGAAGAGAAAGCAAAAGCGATTGCCTTAGTAGCGGCGAGCGAAACGG
+CAGGAGGGCAAACCGAAGTGTTTACACTTCGGGGTTGTAGGACTGCGATATAGGATTAATCATTATAGAAGAATTACCTG
+GGAAGGTAAGCCAAAGAGAGTAACAGCCTCGTATTTAAAATGATAGATTAACCTTAGCAGTATCCTGAGTACGGCGAGAC
+ACGCGAAATCTCGTCGGAATCTGGGAGGACCATCTCCCAACCCTAAATACTCTCTAGTGACCGATAGTGAACCAGTACCG
+TGAGGGAAAGGTGAAAAGCACCCCGGGAGGGGAGTGAAATAGAACCTGAAACCGTGTGCCTACAACAAGTTCGAGCCCGT
+TAATGGGTGAGAGCGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATATGATGCGAGGTTAAGTTGAAGAGACGGAGCC
+GTAGGGAAACCGAGTCTTAATAGGGCGTCATAGTATCATGTTGTAGACCCGAAACCATGTGACCTACCCATGAGCAGGTT
+GAAGGTGAGGTAAAACTCACTGGAGGACCGAACCAGGGCACGTTGAAAAGTGCTTGGATGACTTGTGGGTAGCGGAGAAA
+TTCCAAACGAACTTGGAGATAGCTGGTTCTCTCCGAAATAGCTTTAGGGCTAGCGTCGATGTTAAGTCTCTTGGAGGTAG
+AGCACTGTTTGGGTGAGGGGTCCATCCCGGATTACCAATCTCAGATAAACTCCGAATGCCAACGAGATATAATCGGCAGT
+CAGACTGCGAGTGCTAAGATCCGTAGTCGAAAGGGAAACAGCCCAGACCACCAGCTAAGGTCCCAAAATATATGTTAAGT
+GGAAAAGGATGTGGGGTTGCACAGACAACTAGGATGTTAGCTTAGAAGCAGCTATTCATTCAAAGAGTGCGTAATAGCTC
+ACTAGTCGAGTGACCCTGCGCCGAAAATGTACCGGGGCTAAAACATATTACCGAAGCTGTGGATGACACAAAAGTGTCAT
+GGTAGGAGAGCGTTCTATGTGTGAAGAAGGTGTACCGTGAGGAGCGCTGGAACGCATAGAAGTGAGAATGCCGGTATGAG
+TAGCGCAAGACAGGTGAGAATCCTGTCCACCGTAAGACTAAGGTTTCCAGGGGAAGGCTCGTCCGCCCTGGGTTAGTCGG
+GACCTAAGGAGAGACCGAAAGGTGTATCCGATGGACAACAGGTTGATATTCCTGTACTAGAGTATATAGTGATGGAGGGA
+CGCAGTAGGCTAACTAAACCAGACGATTGGAAGTGTCTGGTCAAACAGTGAGGTGTGATATGAGTCAAATGCTTATATCT
+TTAACATTGAGCTGTGACGAGGAGCGAAGTTTAGTAGCGAAGTTAGTGATGTCACACTGCCAAGAAAAGCTTCTAGCGAT
+ACATATACTCTACCCGTACCGCAAACCGACACAGGTAGTCGAGGCGAGTAGCCTCAGGTGAGCGAGAGAACTCTCGTTAA
+GGAACTCGGCAAAATGGCCCCGTAACTTCGGGAGAAGGGGCGCTGATTTTAGATCAGCCGCAGTGAATAGGCCCAAGCAA
+CTGTTTATCAAAAACACAGCTCTCTGCTAAATCGTAAGATGATGTATAGGGGGTGACGCCTGCCCGGTGCTGGAAGGTTA
+AGAGGAGTGCTTAGCGTAAGCGAAGGTATGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAG
+CGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAATGATTTGGGCACTGTCTCAACGAGAGACTCGGTGA
+AATTTTAGTACCTGTGAAGATGCAGGTTACCCGCGACAGGACGGAAAGACCCCATGGAGCTTTACTGCAGTTTGATATTG
+AGTATCTGTACCACATGTACAGGATAGGTAGGAGCCTATGATAACGGGACGCCAGTTTCGTTTGAGGCGTTGTTGGGATA
+CTACCCTTGTGTTATGGCTACTCTAACCCAGATAGGCAATCCCTATCGGAGACAGTGTCTGACGGGCAGTTTGACTGGGG
+CGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGACTGGTTGGAAATCAGTCGTAGAGTGTAAAGGTA
+TAAGGGAGCTTGACTGCGAGAGCTACAACTCGAGCAGGGACGAAAGTCGGGCTTAGTGATCCGGTGGTTCCGTATGGAAG
+GGCCATCGCTCAACGGATAAAAGCTACCCTGGGGATAACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGGTTT
+GGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCAC
+GCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGTAGGAAATTTGAGAGGATCTGCTCCT
+AGTACGAGAGGACCAGAGTGGACTTACCGCTGGTGTACCAGTTGTCTTGCCAAAGGCATCGCTGGGTAGCTATGTAGGGA
+AGGGATAAGCGCTGAAAGCATCTAAGTGCGAAGCCCACCTCAAGATGAGATTTCCCATGATTTTATATCAGTAAGAGCCC
+TGAGAGATGATCAGGTAGATAGGTTAGGAGTGTAATTGTGGTGACACATTTAGCGGACTAATACTAATAGCTCGAGGACT
+TATCCAAAAAGAGATATTGACAACGTTACGGTTTCTTGTTAGACTATAGATATTCAATTTTGAGTGAATAAGGCTCAATA
+GTTAAGTGATAATTGCCTAGGAGATACACCTGTTCTCATGCCGAACACAGAAGTTAAGCCCTAGAACGCCGGAAGTAGTT
+GGGGGTTGCCCCCTGTGAGATAAGGTAGTCGCTTAGCAAAGGGAGTTTAGCTCAGCTGGGAGAGCATCTGCCTTACAAGC
+AGAGGGTCAGCGGTTCGATCCCGTTAACTCCCATAGGTCCCGTAGTGTAGCGGTTATCACGTCGCCCTGTCACGGCGAAG
+ATCGCGGGTTCGATTCCCGTCGGGACCGTAGACTCGTTAGCTCAGTTGGTAGAGCAATTGACTTTTAATCAATGGGTCAC
+TGGTTCGAGCCCAGTACGGGTCATTTAGAAATGCGGGTGTGGCGGAATTGGCAGACGCACCAGATTTAGGATCTGGCGCT
+TAACGGCGTGGGGGTTCAAGTCCCTTCACCCGCATTAGTAGATTGCCGGCTTAGCTCAGTTGGTAGAGCATCTGATTTGT
+AATCAGAGGGTCGCGTGTTCAAGTCATGTAGCCGGCATTACAATTTTATAGGATAAATAGTGTCTTTAGTGCGAACGTAG
+TTCAGTGGTAGAACATCACCTTGCCAAGGTGAGGGTCGCGGGTTCGAACCCCGTCGTTCGCTTGTTAGAGGCCGGGGTGG
+CGGAACTGGCAGACGCACAGGACTTAAAATCCTGCGATGGTAAACATCGTACCGGTTCGATTCCGGTCCTCGGCATATAA
+TATTTAGCACCCTTAGCTCAACTGGATAGAGTACCTGACTACGAATCAGGCGGTTAGAGGTTCGACTCCTCTAGGGTGCA
+TATTTTTCGGGAAGTAGCTCAGCTTGGTAGAGTACTTGGTTTGGGACCAAGGTGTCGCAGGTTCGAATCCTGTCTTCCCG
+ATGGATATATTTTTATGGCGGTGTAGCTCAGCTGGCTAGAGCGTCCGGTTCATACCCGGGAGGTCGGGGGTTCGATCCCC
+TCCGCCGCTATTTATTTTATTGAGACTTTGGACCTTTAGCTCAACTGGTTAGAGCACTCGGCTCATAACCGAGCGGTCGT
+AGGTTCGAGTCCTACAAGGTCCATATTTTTTGTTATATGGAGGATTACCCAAGTCCGGCTGAAGGGAACGGTCTTGAAAA
+CCGTCAGGCGTGTAAAAGCGTGCGTGGGTTCGAATCCCACATCCTCCTTTAAAGATATCGCGGGATGGAGCAGCTAGGTA
+GCTCGTCGGGCTCATAACCCGAAGGTCGTAGGTTCAAATCCTGCTCCCGCAATAGGCTCGGTAGCTCAGTTGGTAGAGCA
+ATGGATTGAAGCTCCATGTGTCGGCGGTTCGATTCCGTCTCGCGCCATTTATTATATAAGTTTTTAGCGGGTGTAGTTTA
+GTGGTAAAACTACAGCCTTCCAAGCTGTTGTCGCGAGTTCGATTCTCGTCACCCGCTTACTTTACATAAAAGTAAAACCA
+AGCATTTGCTTGGGCGCGTAGCTCAGGTGGTTAGAGCGCACGCCTGATAAGCGTGAGGTCGGTGGTTCGAGTCCACTCGT
+GCCCATTAATATTAATTTGGAGAATTACTCAAGAGGCTGAAGAGGACGGTTTGCTAAATCGTTAGGTCGGGTAACTGGCG
+CAAGGGTTCGAATCCCTTATTCTCCGTAAATATTATAATTTTAAGAGTAATTATACTCTTTTTTTATTTCTCTTTTAGTT
+TCACTATGGAGTAATTATATTGATAGAGTGAATAGAAGAAGGTTATCGTTTTCTAGATTTGATTATGGTTCATTTAGAAA
+TAGTTGATTTCAAATATAAATGTAACAATGACGTAATATAATTTCGTGAATTTTTTGGTAAAATATTTAATGTCTTATCG
+TAAAGGAGTAGTTTAATAAAAATGAAAAAAAGAATATTATCAGCAGTCCTTGTGAGTGGAGTAACTCTTGGAACTGCTGC
+CGTAACAGTAAACGCTGATGACTTTGACTCGAAAATTGCTGCTACTGATTCAGTAATCAATACTTTATCAGGGCAACAAG
+CAGCAGCACAAAACCAGGTGACTGCTATTAAAGGACAAGTTGGTGCTTTAGAGTCTCAACAATCAGAATTAGAAGCGCAA
+AATGCTCAACTTGAGGCTGTATCTCAGCAGTTAGGTCAAGAGATTCAAACTCTTTCTAATAAAATTGTTGCACGTAACGA
+ATCTTTGAAAAAGCAAGTTCGTAGTGCTCAAAAGGGTAACTTGACTAACTATATTAATACTATTTTAAATTCGAAATCAG
+TATCTGATGCTGTTAATCGTGTTGTTGCTATTCGTGAGGTTGTTTCAGCTAATGAAAAGATGTTAGCACAACAAGAGGCT
+GACAAAGCGGCCTTAGAAGCTAAACAAATTGAAAATCAAAATGCTATAAATACTGTAGCAGCTAACAAGCAAGCTATCGA
+AAATAATAAAGCAGCCTTAGCAACACAAAGAGCACAATTAGAAGCAGCTCAATTAGAGTTATCTGCTCAATTGACTACAG
+TCCAAAATGAAAAAGCATCTTTAATTCAGGCAAAAGCACAAGCTGAGGAAGCTGCGCGTAAGGCAGCTGAAGCACAAGCA
+GCAGCTGAAGCGAAAGCACAAGCTGAAGCGAAAGCACAAGCTGAGTCTGTAGCAAAAGCACAGGCAGCAGCACAAGTTGA
+GTCTGCCACAGCTCCTACTGAAACAGTTCAAACACAACCGAGAACTGAAATAAAGCCTTCTAATCTTACGGCTACTTCTT
+CGGCAACTACTGTTGCTACAACTACAGCTACAGCTACTAATGAGCCAAAAGTTACTCAACCTTCTGTAGTAACTAAAGCA
+GTTGAAGCACCTAAAGCAGTTGTTTCTTCAACACCTAGAGCGGTATCAAAACCTGTTGTCAGAAGTTATGATTCAAGTAA
+CACATACCCAATGGGACAATGTACTTGGGGAGCTAAGTCAATGGCTTCTTGGGTTGGTAACTATTGGGGAAATGCTAATC
+AGTGGGGTGCTAGTGCACGTGCAGCTGGTTATTCTGTAGGAACTACCCCTCGTGTTGGTGCAGTAGCTGTTTGGCCATAT
+GATGGTGGTGGTTACGGGCACGTTGCAGTAGTAACGTCAGTGGCTAACAATTCATCTATCCAAGTTATGGAATCAAACTA
+TGCTGGAAATATGAGTATTGGCAATTACCGTGGTTCATTTAACCCTAGTGCTTCTGGCTCTGTTTACTATATTTACCCAA
+ATTAATGAATACTAAGGAGATCTTTCGTGGTCTCCTTTTTGTTTATTAATTAGGTATGGTTTATTTTGGATTGAAAAATT
+GTGTAAAAAGCGTTAAAATGGTATAGGACTAAAGTTTTGGAGGAAATCATGTCTTATTCTAATTTAAAATTGTTTGCACT
+GTCATCAAACAAAGAACTAGCGAAAAAAGTGTCTCAGACGATTGGAATTCCGCTAGGTCAATCGACAGTTCGCCAATTTT
+CTGATGGTGAGATTCAAGTTAATATTGAAGAGTCTATTCGTGGCCATCATGTTTTTATTTTACAATCAACAAGCTCACCA
+GTTAATGATAATTTGATGGAAATTTTAATTATGGTTGACGCTTTAAAGCGTGCTAGTGCGGAGTCTGTTAGTGTGGTAAT
+GCCTTACTATGGGTATGCTCGTCAAGATCGCAAGGCACGTTCTCGTGAACCTATTACTTCGAAACTCGTTGCGAACATGC
+TAGAAGTTGCTGGTGTTGATCGTCTTTTAACAGTTGATTTACATGCAGCTCAAATTCAGGGATTCTTTGATATTCCCGTT
+GATCACCTTATGGGGGCTCCCCTTATTGCAGATTACTTTGATCGTCAGGGATTGGTTGGTGATGATGTTGTTGTCGTTAG
+TCCTGATCATGGTGGCGTAACACGTGCACGTAAGCTGGCACAGTGTTTAAAGACACCGATTGCTATCATTGATAAGCGCC
+GTAGTGTTACTAAAATGAATACATCTGAAGTAATGAATATTATTGGTAATATCAAAGGTAAAAAATGTATTTTAATTGAT
+GATATGATTGATACTGCAGGTACTATTTGCCATGCTGCAGACGCTTTAGCTGAAGCAGGGGCAACAGCGGTTTATGCTTC
+ATGTACTCACCCTGTTTTATCAGGGCCGGCTTTGGATAATATTCAAAATTCAGCTATTGAAAAATTAATTGTGTTAGATA
+CGATTTACCTCCCTGAAGAACGTTTGATTGATAAGATTGAACAAATTTCAATTGCGGAATTGATTGGTGAAGCTATTATC
+CGTATTCACGAGAAACGTCCTTTATCACCATTATTTGAAATGAATAAACTAAAATGACAAAAAACCTGTTATTAACAGGT
+TTTTTATCATTTAATGACGGAAAACTGGACACAAATTATTTTTCTTGTATAATTAAATATATTATTTCTTATCAGGAGGT
+TATGATGACATTAGAGAAACGATTTAATAAGTACTTAGATAGAATAGAGGTCTCCTTAATTCGTCAGTTTGATCAATCTA
+TTTCAGATATACCTGGAATGGTAAAATTAACTCTTGGAGAACCAGATTTTACCACTCCTGATCATGTTAAAGAAGCAGCT
+AAATCAGCTATTGATGCGAATCAATCGTATTACACTGGTATGAGCGGTTTATTAGCTCTAAGGCAAGCTGCTGCAGATTT
+TGCAAAGGATAAATATAATCTTACTTATAATCCTGATTGTGAGATCTTGGTTACGATAGGTGCCACAGAAGCTCTGTCTG
+CATCTCTTATAGCTATTTTAGAAGCTGGTGATGTTGTTCTATTACCTGCCCCCGCTTATCCAGGATATGAGCCAATAGTT
+AACCTTGTAGGAGCTGATATCGTAGAAATTGATACTAGAGAAAATGACTTTAGACTAACTCCTGAAATGTTAGAAACGGC
+TATTATCCAACAAGGTGAAAAATTAAAGGCTGTTTTACTTAATTATCCTACTAACCCTACAGGTATTACCTATTCAAGGC
+AAGAAATTGCTGCATTAGCTGAAGTCCTTAAAAAATATGATATTTTTGTTATTAGTGATGAAGTTTATTCTGAGTTAACT
+TACACTGGTCAGCAGCATGTTTCAATTGCAGAATATTTACCTAACCAAACTATCTTAATTAATGGCTTATCAAAATCACA
+TGCTATGACTGGTTGGAGAGTTGGATTGGTGTATGCTCCTGAAGCATTTATTGCTCAAATCATTAAAAGTCATCAATACA
+TGGTGACAGCTGCTAGTACTATTTCGCAATTTGCTGGGGTAGAAGCCTTATCTGTGGGTAAAAATGATACGTTACCTATG
+CGTCAAGGATATATTAAACGTAGAGATTATATCATTGATAAAATGTCTAAACTTGGTTTCAAAATAATTAAACCGAGTGG
+CGCTTTTTATATCTTTGCTAAAATACCTGATAGCTATCCACAGGATTCTTTCAAGTTTTGTCAGGATTTTGCTTATCAAC
+AAGCTGTAGCTATTATTCCAGGAGTGGCTTTTGGTAAATATGGTGAAGGATATATACGTCTTTCTTATGCTGCTAGTATG
+GAAGTTATTGAAACAGCAATGGCTAGATTGAAAGTTTTTATGGAATCATATGAGGGTTAGTCAAACATACGGTCTCGTTT
+TGTATAATCGTAATTATCGTGAAGATGATAAATTAGTTAAAATCTTTACGGAGACTGAGGGGAAAAGGATGTTTTTTGTA
+AAGCATGCTTCAAAGTCAAAATTCAATGCTGTGCTCCAACCTTTGACTATTGCTCATTTTATTTTAAAAATTAATGATAA
+TGGTCTTTCTTATATTGATGATTATAAAGAAGTTTTAGCATTTCAAGAAACCAATTCAGACTTGTTTAAGTTGTCATATG
+CGAGTTATATTACTTCTTTGGCTGATGTGGCTATTAGTGATAATGTAGCGGATGCTCAATTATTTATTTTCCTAAAGAAA
+ACGTTAGAATTGATTGAGGACGGTTTAGATTATGAGATTCTAACGAATATTTTTGAAGTACAACTACTAGAGAGGTTCGG
+TGTTGCTTTAAATTTTCATGATTGTGTTTTTTGTCATAGGGTAGGATTACCTTTTGATTTTTCACACAAATATTCTGGAT
+TATTATGTCCAAACCATTATTATAAAGACGAGAGAAGAAACCACCTAGATCCTAATATGCTGTACTTAATCAATCGTTTT
+CAGTCAATTCAATTTGATGATTTACAAACAATTTCTGTGAAACCTGAGATGAAACTTAAAATTCGTCAATTTTTGGACAT
+GATTTACGATGAATATGTAGGGATTCATCTTAAAAGTAAAAAATTTATTGATGATTTGTCTAGTTGGGGAAGTATTATGA
+AATCAGATTAAGTTGTAAAGAGGAACATGACATTAGTGTCATGTTCTTTTTTTTAATATTAGGATAAACTAATATGGAAT
+TAATTTTTAGGATATTTGAGATGAAAAAAACATTATACATTACCAATAAACTCTTTTTTGCTAACTGGTTTGTGCCAGTT
+ATTGGTGCAGTTCTAATTCAAGTTATCGGCATCATTGTAAGTAGACGCCTTGTAGTAAAATTGCTACCTGATGATTATAA
+ATTCAATTTATACATTGCGCTTTTACTATTTGTTCCTATTTTGGCAAGTATTTTACTATTTTTAATCTATTTTCAAAAAA
+GGGATTTTACTTCCTTGGGATTTACTAAAGATAATAATGTTTTAACAACGATCTCAGGATTTATTACTGGTAGTTTACTG
+ATGTTTTTTATTTATATTTGCCACTGGTTATCAGGTTTTGTGGAAATTTCTTCCAGCAATTCCTTTTCTTTTGGACCTTT
+TTTCTTTTTATTTCTTGCATACTTTATCCAAAGCTTGACAGAGGAAATTTTATTTAGAGGATATGTTATGACAACAGTTA
+CCAAATTTAAAGGTAGTTTTGCAGGTGTTTTATGTAATTCTATGTTGTTTTCTTTTATCCACTTTAGAAACTATGGTATC
+ACAGCAATAGCACTTTTTAATTTATTTTTACTTGGTATTATTTTTTCTATTCTTTTTAATATGACCAAAAATATTCTTTT
+TGTTACAGGAGTTCATACTACATGGAATTTTACTATGGGATGTGTATTAGGTAATAAGGTTAGTGGGGGGGATTCTCCTG
+TTTCTCTTTTTAGAATTACTGAAAATTCTAGCTTTGCTCTTTGGAATGGTGGGGATTTTGGTTTTGAAGGGGGAGTACTA
+TGTTCTTTGATATTAGTAGGTTGTTTAGCATACTTTTCTTTGGAAAGCGTGAGAGTATCTGTTAGATATTAGCTATTATT
+GCCTTCTTGTGAAAAAAATAAAGAAACGTGCTATAATATAGCCACTAAGTTTTTATGAGGAGTTCATTCATGAAGAAAAT
+TGCTATAGATGCTATGGGTGGAGATTACGCTCCCAAAGCTATTGTAGAGGGTGTTAATCAAGCTATTTCAGATTTTAGTG
+ATATTGAAGTACAACTCTATGGCGATCAGAAAAAAATTGAGAAATATTTAACAGTAACGGAGCGAGTTAGTATTATTCAT
+ACTGAAGAAAAAATTAATTCTGATGATGAGCCTGCTAAAGCTGTTCGTCGTAAAAAACAGTCTTCGATGGTCTTAGGAGC
+TAAGGCAGTCAAAGATGGTGTTGCACAGGCCTTTATTTCTGCAGGGAATACAGGAGCTTTATTAGCTGCTGGTTTGTTTG
+TAGTAGGACGTATAAAAGGTGTTGATCGACCAGGCTTAATGTCAACTATGCCTACGTTAGATGGTGTGGGTTTTGATATG
+CTTGATTTAGGAGCTAATGCAGAAAACACAGCTTCTCATCTTCATCAATATGCTATTTTAGGGTCGTTTTATGCAAAAAA
+TGTCCGTGGTATTGAAGTTCCTCGTGTAGGTCTCTTAAATAACGGAACGGAAGAAACAAAAGGCGATTCTCTTCATAAAG
+AAGCTTATGAACTGTTAGCAGCAGAGCCTTCTATTAATTTTATTGGAAATATTGAAGCACGTGATTTGATGTCTAGTGTA
+GCAGATGTTGTTGTCACTGATGGTTTTACTGGAAATGCTGTTCTAAAGACAATGGAAGGTACAGCTATGAGTATTATGGG
+AAGCCTAAAATCTTCAATTAAATCAGGTGGCGTGAAAGCTAAATTAGGAGCACTTCTATTAAAAGATAGCCTATATCAGC
+TAAAAGATAGTATGGACTATTCAAGCGCGGGTGGAGCGGTTCTTTTTGGTTTAAAAGCTCCAATAGTAAAATGCCATGGA
+TCAAGTGATTCTAAAGCTGTTTATTCTACTTTGAAGCAAGTTCGTACAATGTTGGAAACTCAAGTAGTTGATCAATTAGT
+TGATGCCTTTACAGATGAATAGGAGTGAACTCATGTCAAGAGATGAAGTTTTTGAAAAGATGCTGGAATTATTAAGGCAG
+CAACTTGGTGACCCACAGTTAGATATCACACCAGAGTCATCGTTACATGATGATTTAGCAATTGACTCTATCGCTTTAAC
+AGAGTTTATTATCAATTTGGAAGATGTGTTTCATCTAGAGATTCCAGATGAGGCTGTCGAACACATGTCAAGCGTCCAAC
+AACTATTAGATTATATCATTGAACATAAGTAATAATAAAAAGGAAGAAAATACGAACGTTTCTTCTTTTTTTTGATTTTA
+AATAAAGTTTTTGTTGTATTAGATAATGTTGTGTGTTAGAATAACTCTTAAAATAAGAGAAAGGCGAATAATCAAGTGAC
+TAACCAGCTTATTTATACAGGAAAAGCGAAAGATATTTATAGTACAAAAGATGAAAATGTGATTAGAACGGTCTATAAAG
+ACCAAGCTACTATGTTGAATGGAGCTCGTAAGGAGACTATTGATGGCAAGGGAGCACTAAATAATCAGATTTCATCTCTT
+ATTTTTGAGAAATTAAATATGGCTGGTGTGGTGACACATTATATTGAGCAAATTTCAAAAAACGAACAATTGAATAAAAA
+AGTTGATATTATTCCACTTGAGGTGGTGCTACGGAATGTGACAGCAGGCTCATTTTCAAAACGTTTTGGAGTGGAAGAAG
+GACACGTTCTTGAAACGCCAATCGTGGAATTTTACTACAAAAATGATAATCTGAATGATCCTTTTATCAATGATGAGCAT
+GTGAAGTTTTTGGGTATTGTTAATGATGAGGAGATTGCTTATCTGAAAGGAGAGACTCGCCATATTAATGAACTCTTGAA
+AGATTGGTTTGCTCAGATTGGGCTTAACTTGATTGACTTCAAGTTGGAGTTCGGATTTGACAAGGATGGCAAAATCATCT
+TGGCTGATGAGTTCTCACCTGACAACTGCCGTCTCTGGGATGCTGATGGTAATCATATGGACAAGGATGTTTTTCGTAGG
+GATCTTGGTAGCTTGACCGATGTCTATCAAGTTGTACTTGAGAAGTTGATAGCATTGTAATTAGAAGAGGAAGGAATTGA
+ATCCGTTCGGGAAACTCAGAAAAAAGATTGGGCTTACTGAAATCTCAATTTCAGACGTCCTCCTATTTTCGAGTCGCTCC
+CTTGTCGGACTTGGTATCTTATATGAATAAACGTATTTTTGTTGAGAAAAAGGCTGACTTTGGCATTAAATCGGCTAGTC
+TTGTGAAAGAGTTGACGCATAATCTACAACTGGCTTCTTTGAAGGATTTGCGTATCGTGCAGGTCTATGATGTCTTCAAT
+TTGGCTGAGGATTTGCTGGCGCGTGCTGAGAAGCATATTTTCTCTGAGCAGGTGACAGACCGTCTTTTGACAGAAGCTGA
+AATCACTGCGGAGCTTGATAAGGTTGCCTTCTTTGCCATTGAGGCGCTTCCTGGTCAATTTGACCAACGTGCTGCTAGTT
+CGCAAGAAGCTTTGCTATTGCTTGGAAGTGACAGTCAGGTCAAGGTCAATACAGCTCAGCTTTACTTGGTCAATAAGGAT
+ATTGCAGAAGCAGAGCTTGAAGCCGTTAAGAACTATCTTTTGAATCCCGTTGATTCACGTTTCAAGGATATTACCTTGCC
+ACTTGAAGTGCAGGCTTTCTCTGTGTCTGATAAGACAATCTCTAATCTTGATTTCTTCGAAACTTATCAGGCTGACGATT
+TTGCAGCCTATAAGGCAGAGCAGGGATTGGCTATGGAGGTCGATGACCTTCTCTTCATCCAAGATTATTTCAAATCAATC
+GGGCGTGTGCCAACTGAGACTGAGTTGAAAGTTTTGGATACGTATTGGTCAGACCACTGCCGTCACACAACCTTTGAAAC
+TGAATTGAAAAACATTGATTTTTCGGCCTCTAAATTCCAAAAACAATTGCAGGCGACTTATGACAAATACATTGCCATGC
+GTGATGAGCTTGGTCGTTCTGAAAAGCCGCAGACACTTATGGATATGGCGACTATCTTTGGTCGTTATGAGCGTGCCAAT
+GGTCGTCTGGACGATATGGAAGTCTCAGATGAAATCAATGCCTGCTCAGTTGAAATTGAAGTAGATGTTGATGGTGTGAA
+AGAGCCTTGGCTCCTCATGTTTAAGAACGAGACTCACAACCACCCAACAGAAATTGAGCCATTTGGTGGAGCGGCGACTT
+GTATCGGTGGTGCCATTCGTGACCCATTGTCAGGACGTTCATACGTTTATCAGGCTATGCGTATTTCAGGCGCAGGAGAT
+ATCACGACTCCGATTGCGGAAACACGTGCTGGTAAATTGCCACAACAGGTTATTTCTAAGACTGCGGCGCACGGCTATTC
+TTCATATGGTAACCAAATTGGGCTTGCGACAACTTATGTGCGTGAGTACTTCCACCCTGGCTTCGTAGCTAAACGCATGG
+AGCTTGGAGCTGTGGTTGGTGCTGCACCTAAGGAAAATGTGGTTCGTGAAAAACCAGAGGCAGGCGATGTGGTTGTCTTG
+CTCGGTGGTAAAACAGGTCGTGACGGTGTCGGCGGTGCGACAGGTTCATCTAAGGTTCAAACGGTTGAATCTGTGGAAAC
+AGCTGGCGCAGAGGTACAAAAAGGGAATGCCATCGAAGAACGTAAGATTCAACGCCTTTTCCGTGATGGTAATGTCACTC
+GCCTAATCAAGAAATCAAATGACTTCGGTGCAGGTGGTGTCTGTGTTGCCATCGGTGAATTAGCTGATGGTCTTGAAATC
+GATTTGGACAAGGTGCCACTTAAATACCAAGGTCTTAATGGTACTGAAATTGCTATCTCAGAATCTCAAGAAAGGATGTC
+AGTTGTTGTTGGTCCAAGTGATGTGGATGCCTTCATCGCAGCCTGTAACAAGGAAAATATCGATGCAGTTGTTGTTGCGA
+CAGTTACTGAAAAACCAAATCTTGTCATGACTTGGAATGGTGAAACAATTGTTGATTTGGAACGCTGTTTCCTTGATACC
+AACGGTGTTCGTGTCGTAGTTGATGCCAAAGTCGTTGACAAGGACTTAACAGTTCCAGAAGCGCGCACAACATCAGCAGA
+GACACTTGAAGCAGATATGCTTAAGGTCTTGTCTGACCTCAATCACGCTAGTCAAAAAGGTCTTCAAACTATCTTTGACT
+CATCTGTTGGTCGTTCAACCGTTAACCACCCAATCGGTGGTCGTTACCAAATCACACCGACAGAAAGTTCTGTTCAAAAA
+TTGCCAGTTCAATATGGTGTGACAACAACAGCATCTGTTATGGCTCAAGGTTACAATCCTTATATTGCAGAGTGGTCACC
+TTATCACGGTGCTGCCTATGCTGTTATTGAAGCGACAGCTCGCTTGGTAGCAACGGGTGCTGACTGGTCTCGTGCACGTT
+TCTCTTACCAAGAGTATTTCGAGCGTATGGATAAACAGGCAGAGCGTTTTGGTCAGCCAGTATCAGCTCTTCTTGGTTCT
+ATTGAGGCTCAGATTCAATTTGGTTTGCCATCAATCGGCGGTAAGGACTCTATGTCTGGTACTTTCGAAGAATTGACAGT
+ACCACCAACCTTGGTAGCTTTCGGTGTGACAACAGCGGACAGCCGCAAGGTTCTCTCTCCTGAGTTTAAAGCGGCTGGTG
+AGAATATCTACTACATTCCAGGTCAAGCTATTTCAGAAGATATTGATTTTGACCTTATCAAGGCTAACTTTAGCCAGTTT
+GAGGCTATTCAAGCTCAACATAAGATTACCGCTGCCTCAGCCGTTAAATACGGTGGTGTCCTAGAAAGTCTTGCTCTCAT
+GACTTTTGGTAACCGTATCGGTGCTTCTGTTGAAATTGCAGAGCTTGACAGCAGCTTGACAGCTCAACTCGGAGGCTTTG
+TCTTTACATCAGTTGAGGAAATTGCTGACGTTGTGAAGATCGGTCAAACTCAGGCAGACTTTACAGTCACTGTCAATGGA
+AATGACCTAGCTGGTGCAAGCCTTCTATCAGCCTTCGAAGGTAAATTAGAAGAAGTTTACCCAACAGAGTTTGAACAGGT
+AGATGCTATTGAGGAAGTTCCTGCTGTGGTATCAGATGTTGTTATCAAGGCTAAGGAAATTATTGAAAAACCAGTAGTTT
+ACATCCCAGTCTTTCCTGGTACTAACTCAGAGTACGATTCAGCTAAGGCCTTTGAACAGGTTGGAGCTAGCGTCAACTTG
+GTGCCATTTGTAACCTTGAATGAGGCTGCTATTGCTGAGTCAGTTGATACGATGGTTGCTAATATTGCTAAGGCAAATAT
+CATCTTCTTTGCTGGAGGTTTCTCAGCAGCGGATGAACCAGATGGCTCTGCTAAGTTTATCGTCAATATCTTGCTTAACG
+AGAAGGTTCGCGCAGCTATTGACAGCTTCATCGAAAAAGGTGGCCTTATCATCGGTATCTGTAATGGTTTCCAAGCCCTT
+GTTAAATCAGGTCTTCTTCCATACGGAAACTTCGAGGAAGCTGGTGAGACAAGTCCAACCCTCTTCTATAACGATGCTAA
diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
new file mode 100644
index 0000000000000000000000000000000000000000..9998c414977225cf67611108501531b9cb103cf8
GIT binary patch
literal 31097
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HcmV?d00001


From e31b5f966bb622564cc014d0173e9b5c51dd9638 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 21 Mar 2024 16:58:53 +0100
Subject: [PATCH 02/97] update macros

---
 tools/chewbbaca/CreateSchema.xml |  2 +-
 tools/chewbbaca/macros.xml       | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 6f583e5acfb..7e0507e6c95 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -1,4 +1,4 @@
-<tool id="CreateSchema" name="chewBBACA CreateSchema" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="CreateSchema" name="chewBBACA CreateSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Create a gene-by-gene schema</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/chewbbaca/macros.xml b/tools/chewbbaca/macros.xml
index ffe84c0c009..4a79d108203 100644
--- a/tools/chewbbaca/macros.xml
+++ b/tools/chewbbaca/macros.xml
@@ -1,15 +1,15 @@
 <macros>
+    <token name="@CHEW_VERSION@">3.3.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@CHEW_VERSION@">chewBBACA</requirement>
-            <requirement type="package" version="@BLAST_VERSION@">blast</requirement>
-            <requirement type="package" version="@ZIP_VERSION@">zip</requirement>
+            <requirement type="package" version="@CHEW_VERSION@">chewbbaca</requirement>
+            <requirement type="package" version="2.15.0">blast</requirement>
+            <requirement type="package" version="3.0">zip</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@CHEW_VERSION@">1.15.1</token>
-    <token name="@BLAST_VERSION@">1.15.1</token>
-    <token name="@ZIP_VERSION@">1.15.1</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">

From 9c403c76314b7c221559563f6952d0fb2745688c Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 21 Mar 2024 17:22:23 +0100
Subject: [PATCH 03/97] add compare by sim_size for zip files

---
 tools/chewbbaca/CreateSchema.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 7e0507e6c95..00e55dfac3c 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -56,7 +56,7 @@
     <tests>
         <test expect_num_outputs="1">
         <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
-        <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+        <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[

From 1c22e19d6dbbe462422857fcaa0a39b2e4e8b213 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 22 Mar 2024 13:30:29 +0100
Subject: [PATCH 04/97] 3rd tool PrepExternalSchema

---
 tools/chewbbaca/PrepExternalSchema.xml | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 tools/chewbbaca/PrepExternalSchema.xml

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
new file mode 100644
index 00000000000..f2f39c3bfe4
--- /dev/null
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -0,0 +1,22 @@
+<tool id="PrepExternalSchema" name="Adapt an external schema to be used with chewBBACA (chewBBACA.py)" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py PrepExternalSchema -g schema -o output
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+        /bin/sh: 1: chewBBACA.py: not found
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

From b38e5c79030df2716287aa718015216e3444a047 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 10:31:22 +0100
Subject: [PATCH 05/97] Change to min value of --l

---
 tools/chewbbaca/AlleleCall.xml   | 2 +-
 tools/chewbbaca/CreateSchema.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 01084671bcb..9732534febf 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -30,7 +30,7 @@
         <section name="advanced" title="Advanced options">
             <param argument="--training_file" type="data" format="binary" label="Prodigal training file" optional="true" />
             <param argument="--blast_score_ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
-            <param argument="--minimum_length" type="integer" min="1" value="201" label="Minimum sequence length value"/>
+            <param argument="--minimum_length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
             <param argument="--translation_table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
             <param argument="--size_threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
             <param argument="--no-inferred" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Add the sequences of inferred alleles (INF) to the schema" help="Use this parameter if the schema is being accessed by multiple processes/users simultaneously." />
diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 00e55dfac3c..bbf6fc1735f 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -27,7 +27,7 @@
         <section name="advanced" title="Advanced options">
             <param argument="--training_file" type="data" format="binary" label="Prodigal training file" optional="true" />
             <param argument="--blast_score_ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
-            <param argument="--minimum_length" type="integer" min="1" value="201" label="Minimum sequence length value"/>
+            <param argument="--minimum_length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
             <param argument="--translation_table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
             <param argument="--size_threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
             <param argument="--prodigal_mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">

From f1b2d853fbed17cbef225c7ec4eb818c5a8c7fd8 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 10:33:10 +0100
Subject: [PATCH 06/97] Add PrepExternalSchema tool from chewbbaca

---
 tools/chewbbaca/PrepExternalSchema.xml        |  55 ++++++++++++++++--
 .../GCA_000007265.1_ASM726v1_schema_seed.zip  | Bin 31097 -> 31097 bytes
 2 files changed, 51 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index f2f39c3bfe4..b36083f1f09 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -1,22 +1,69 @@
-<tool id="PrepExternalSchema" name="Adapt an external schema to be used with chewBBACA (chewBBACA.py)" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="PrepExternalSchema" name="chewBBACA PrepExternalSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Adapt an external schema to be used with chewBBACA</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        chewBBACA.py PrepExternalSchema -g schema -o output
+        mkdir ./schema &&
+        unzip $input_schema -d ./schema &&
+        chewBBACA.py PrepExternalSchema
+            #if str($advanced.training_file) != 'None'
+                --ptf '$advanced.training_file'
+            #end if            
+            --bsr $blast_score_ratio
+            --l $minimum_length
+            --t $translation_table
+            --st $size_threshold
+            #if str($advanced.size_filter) == 'true'
+                --size-filter
+            #end if
+            --size-filter $size_filter
+            -g ./schema/schema_seed/ -o ./schema_seed &&
+        zip -r PExternalschema_seed.zip ./schema_seed
     ]]></command>
     <inputs>
+        <param format="zip" name="input_schema" type="data" multiple="True" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <section name="advanced" title="Advanced options">
+            <param argument="--training_file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--blast_score_ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
+            <param argument="--minimum_length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
+            <param argument="--translation_table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
+            <param argument="--size_threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+            <param argument="--size-filter" type="boolean" truevalue="" falsevalue="" checked="false" label="Size filter" help="Apply the minimum length and size threshold values to filter out alleles during schema adaptation" />
+        </section>
     </inputs>
     <outputs>
+        <data format="zip" name="schema" from_work_dir="PExternalschema_seed.zip" label="${tool.name} on ${on_string}: PrepExternal Schema files"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
+            <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <output name="schema" file="GCA_000007265.1_ASM726v1_PExternalschema_seed.zip" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
-        /bin/sh: 1: chewBBACA.py: not found
 
+        --ptf, --training-file     (Optional) Path to the Prodigal training file that will be included in
+                                the adapted schema (default: None).
+
+        --bsr, --blast-score-ratio (Optional) The BLAST Score Ratio value that will be used to adapt
+                                the external schema (default: 0.6).
+
+        --l, --minimum-length      (Optional) Minimum sequence length accepted. Sequences with a length
+                                value smaller than the value passed to this argument will be discarded
+                                (default: 0).
+
+        --t, --translation-table   (Optional) Genetic code to use for CDS translation. Must match the
+                                genetic code used to create the training file (default: 11).
+
+        --st, --size-threshold     (Optional) CDS size variation threshold. At the default value of
+                                0.2, alleles with size variation +-20 percent when compared to the
+                                representative will not be included in the final schema (default:
+                                0.2).
+
+        --size-filter              (Optional) Apply the minimum length and size threshold values to
+                                filter out alleles during schema adaptation (default: False).
     ]]></help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file
diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
index 9998c414977225cf67611108501531b9cb103cf8..3bb732668c589ba07e51e9261b8e4eaeeb5137a1 100644
GIT binary patch
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From d22ff0c778cca7f70351a830bb7af6c52230ad6a Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 17:16:42 +0100
Subject: [PATCH 07/97] Some minor adjustment to xmls. create  output of
 allelecall in test-data

---
 tools/chewbbaca/AlleleCall.xml   | 37 +++++++++++++++++++++-----------
 tools/chewbbaca/CreateSchema.xml | 20 ++++++++---------
 2 files changed, 34 insertions(+), 23 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 9732534febf..d85160374e0 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -12,29 +12,30 @@
         #end for
         unzip $input_schema -d ./schema &&
         chewBBACA.py AlleleCall
-            #if str($advanced.training_file) != 'None'
-                --ptf '$advanced.training_file'
+            #if str($training_file) != 'None'
+                --ptf $training_file
             #end if            
             --bsr $blast_score_ratio
             --l $minimum_length
             --t $translation_table
             --st $size_threshold
+            $no_inferred
             --pm $prodigal_mode
             --mode $mode
             --force-continue
             -i ./input -g ./schema/schema_seed/ -o ./output
     ]]></command>
     <inputs>
-        <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
-        <param format="zip" name="input_schema" type="data" multiple="True" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <param format="fasta" name="input_file" type="data" multiple="true" label="Genome assemblies in FASTA format"/>
+        <param format="zip" name="input_schema" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
-            <param argument="--training_file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--blast_score_ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
-            <param argument="--minimum_length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
-            <param argument="--translation_table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
-            <param argument="--size_threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
-            <param argument="--no-inferred" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Add the sequences of inferred alleles (INF) to the schema" help="Use this parameter if the schema is being accessed by multiple processes/users simultaneously." />
-            <param argument="--prodigal_mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">
+            <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
+            <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
+            <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
+            <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+            <param argument="--no-inferred" type="boolean" truevalue="--no-inferred" falsevalue="" checked="false" label="Add the sequences of inferred alleles (INF) to the schema" help="Use this parameter if the schema is being accessed by multiple processes/users simultaneously." />
+            <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">
                 <option value="single" selected="true">
                         single
                     </option>
@@ -62,7 +63,8 @@
         <test>
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
-            <output_collection name="allelecall_results">
+            <output_collection name="allelecall_results" type="list">
+                <element name="loci_summary_stats" file="loci_summary_stats.tsv" compare="sim_size"/>
                 <element name="paralogous_loci" ftype="tabular">
                     <assert_contents>
                         <has_text_matching expression="Genome.*Loci.*CDS"/>
@@ -70,10 +72,19 @@
                 </element>
                 <element name="results_alleles" ftype="tabular">
                     <assert_contents>
-                        <has_text_matching expression="1.*1.*NIPHEM.*NIPH.*1.*1"/>
+                        <has_text_matching expression="1.*1.*NIPHEM.*1.*1"/>
                         <has_text_matching expression="GCA_000007265.*1"/>
                     </assert_contents>
                 </element>
+                <element name="results_alleles" file="results_alleles.tsv" compare="sim_size"/>
+                <element name="results_statistics" file="results_statistics.tsv" compare="sim_size"/>
+            </output_collection>
+            <output_collection name="allelcall_log" type="list">
+                <element name="logging_info" ftype="txt">
+                    <assert_contents>
+                        <has_text_matching expression="Used a BSR of: 0.6"/>
+                    </assert_contents>
+                </element>
             </output_collection>
         </test>
     </tests>
diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index bbf6fc1735f..fc665adcd98 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -10,8 +10,8 @@
         cp $file ./input/${file.element_identifier} &&
         #end for
         chewBBACA.py CreateSchema 
-            #if str($advanced.training_file) != 'None'
-                --ptf '$advanced.training_file'
+            #if str($training_file) != 'None'
+                --ptf '$training_file'
             #end if
             --bsr $blast_score_ratio
             --l $minimum_length
@@ -25,12 +25,12 @@
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
         <section name="advanced" title="Advanced options">
-            <param argument="--training_file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--blast_score_ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
-            <param argument="--minimum_length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
-            <param argument="--translation_table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
-            <param argument="--size_threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
-            <param argument="--prodigal_mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">
+            <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--blast_score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
+            <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
+            <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
+            <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+            <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">
                 <option value="single" selected="true">
                         single
                     </option>
@@ -40,8 +40,8 @@
             </param>
         </section>
         <section name="output" title="Output options">
-            <param name="show_cds_invalid" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output invalid CDS file?"/>
-            <param name="show_cds_coord" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output CDS coordinates File?"/>
+            <param name="show_cds_invalid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output invalid CDS file?"/>
+            <param name="show_cds_coord" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output CDS coordinates File?"/>
         </section>
     </inputs>
     <outputs>

From 87386a994f1ed19cbd0b59fedd07ab2e1e1bd043 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 17:20:44 +0100
Subject: [PATCH 08/97] update test-data

---
 .../GCA_000007265.1_ASM726v1_genomic.fna      | 1000 +++++++++++++++++
 .../GCA_000007265.1_ASM726v1_schema_seed.zip  |  Bin 31097 -> 115704 bytes
 2 files changed, 1000 insertions(+)

diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_genomic.fna b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_genomic.fna
index c6394b7578c..5312e4b628f 100644
--- a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_genomic.fna
+++ b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_genomic.fna
@@ -498,3 +498,1003 @@ GTGCCATTTGTAACCTTGAATGAGGCTGCTATTGCTGAGTCAGTTGATACGATGGTTGCTAATATTGCTAAGGCAAATAT
 CATCTTCTTTGCTGGAGGTTTCTCAGCAGCGGATGAACCAGATGGCTCTGCTAAGTTTATCGTCAATATCTTGCTTAACG
 AGAAGGTTCGCGCAGCTATTGACAGCTTCATCGAAAAAGGTGGCCTTATCATCGGTATCTGTAATGGTTTCCAAGCCCTT
 GTTAAATCAGGTCTTCTTCCATACGGAAACTTCGAGGAAGCTGGTGAGACAAGTCCAACCCTCTTCTATAACGATGCTAA
+CCAGCACGTTGCAAAGATGGTTGAGACTCGTATCGCAAATACCAATTCACCTTGGTTGGCAGGAGTTGAGGTCGGCGATA
+TTCATGTCATTCCAGTTTCACACGGTGAAGGTAAATTTGTTGTCAGCGCTTCTGAATTTGCAGAGCTAAGAGACAATGGT
+CAAATCTGGAGCCAATATGTGGACTTTGACGGACAACCATCTATGGATTCTAAATACAATCCAAACGGCTCTGTCAATGC
+CATCGAAGGGATTACCAGCAAGAATGGTCAAATCATCGGTAAGATGGGGCACTCAGAACGCTGGGAAGACGGACTCTTCC
+AAAATATCCCTGGAAACAAAGACCAAAAACTCTTTGAAAGTGCTGTAAAATACTTTACAGGGAAGTGAGAGTGGGACAAA
+AATCGGTAATTCCAAAGGAATTCGATTTTGTCGTCCCCCTCCGCACAGTTGAGTGGGGCTGTAAGAGTTGATTTATCAGC
+GAATTAGAGCCCACTCAACCCCTACGTTTTGCGAACTAGATTATAAAAAATATGGAGGCTTAGGACTTTTGTCCTAGCTT
+TAGCCCTCGCCTTGAATTAGTGAAGGCGAGGTTAGATAGAAATTCGCTATCTTTTGAACGAAGCGAGCTTAACCGTATCT
+TTCCGCCGTATTGGTATTTGGGAGTCATTGAGACTAAGGTTCAATGGCTAGCTTGATAGATTTTCTATTTTAATGTTGGC
+ATTGATGACGACAGATCCAAAATTGAGAAAATCATCAAAGCTACTTAAGAAGAGATACAAAAAGAATTAGGAAAAAAGAA
+TGACATACGAAGTAAAATCTCTAAATGAAGAATGTGGAGTCTTTGGTATCTGGGGGTATCCTCAGGCAGCTCAAGTCACT
+TACTTTGGGCTTCATAGCCTTCAACATCGCGGTCAAGAAGGAGCTGGTATTATTTCAAATGATAATGGGAAACTCTATGG
+TTATCGAAATGTTGGGCTCCTTTCTGAAGTTTTTAAGAATCAATCTGAATTAGATAATTTAACTGGGAATGCGGCTATTG
+GACATGTTCGGTATGCTACTGCAGGTTCTGCAGATATTCGCAATATTCAGCCTTTTCTTTATAAATTTCATGATGGGCAA
+TTTGCTTTATGTCATAATGGTAATTTGACAAATGCTATTTCCTCAAGGAAAGAATTAGAAAAGCAAGGTGCAATTTTCAA
+TGCCTCCTCAGATACTGAAATTTTAATGCATTTGATTCGTCGAAGCCATAACCCAAGTTTTATGGGGAAGGTAAAAGAAG
+CTTTAAGCACTGTAAAGGGAGGTTTCGCCTATCTACTGATGACAGAAGATAAATTAATTGCTGCTCTTGACCCTAATGCC
+TTTCGTCCTTTGTCAATTGGACAAATGCAAAATGGTGCCTGGGTTATTTCCAGTGAGACCTGTGCTTTTGAGGTGGTAGG
+CGCAAAATGGGTTAGAGATGTTGAACCTGGTGAAGTTATTCTTATAGACGATAGTGGTATTCAATGTGATCGTTATACTG
+ATGAAACGCAACTGGCAATTTGTTCGATGGAATATGTCTATTTTGCAAGGCCGGATTCAACTATACATGGTGTTAATGTT
+CATACGGCTCGAAAAAATATGGGAAAGCGTCTTGCACAAGAATTTAAACAGGATGCTGATATTGTAATTGGTGTCCCAAA
+TTCGTCCTTATCGGCTGCTATGGGCTTTGCTGAAGAATCCGGATTACCAAATGAGATGGGCCTTGTAAAAAATCAGTATA
+CGCAGCGAACCTTTATTCAACCGACACAAGAATTAAGGGAACAAGGTGTTCGAATGAAATTATCAGCGGTATCTGGTGTT
+GTCAAAGGAAAGCGCGTTGTTATGATTGATGACTCAATTGTAAGAGGAACGACTTCTAGAAGGATTGTAGGATTATTAAG
+AGAAGCAGGAGCTACTGAAGTACATGTTGCTATAGCTAGTCCAGAATTAAAGTATCCTTGTTTTTATGGAATTGATATTC
+AAACAAGACGAGAATTAATTTCAGCAAATCACGCTGTTGACGAAGTGTGTGATATTATTGGCGCAGATAGTCTAACTTAT
+CTATCAATCGATGGGTTAATTAAATCAATTGGACTCGAAACAAAAGCACCAAATGGTGGTTTATGCGTAGCTTACTTTGA
+TGGACATTATCCAACACCGCTTTATGATTATGAAGAAGAATACCTCAGAAGTTTAGAAGAAAAAACAAGTTTTTATATTC
+AAAAAGTGAAATAAGCTCTGCTAATTATATAAGGAGAAAACATGTCTGAAAAAAATGCTTATGCCCAGTCTGGTGTTGAT
+GTAGAAGCGGGCTACGAAGTTGTCGAACGTATCAAGAAACACGTTGCTCGCACAGAACGTGCTGGTGTCATGGGAGCTCT
+CGGTGGCTTTGGTGGTATGTTTGACCTGTCACAAACAGGTGTTAAAGAACCTGTCTTGATTTCAGGGACTGACGGTGTCG
+GAACTAAACTCATGCTTGCTATCAAGTACGACAAGCACGACACAATCGGTCAAGACTGTGTTGCCATGTGTGTCAACGAT
+ATTATTGCAGCAGGTGCTGAGCCCCTTTACTTCCTTGACTATGTCGCGACTGGTAAAAACGAACCTGCCAAATTGGAACA
+GGTTGTCGCTGGTGTTGCTGAAGGTTGTGTTCAAGCTAGCGCAGCTCTTATCGGTGGTGAAACGGCTGAGATGCCTGGTA
+TGTATGGCGAAGATGATTATGACCTTGCAGGCTTTGCTGTTGGTGTGGCTGAAAAATCTCAAATCATCGACGGTTCAAAG
+GTAAAAGAAGGGGATATTCTTCTTGGACTTGCTTCAAGTGGTATCCATTCAAATGGTTATTCATTGGTACGTCGTGTCTT
+TGCTGACTACACTGGTGATGAGGTGCTTCCAGAGCTTGAAGGCAAACAACTCAAGGATGTCCTTCTTGAGCCAACTCGTA
+TCTATGTTAAAGCAGCTCTGCCATTGATCAAGGAAGAACTAGTTAACGGTATCGCCCACATCACGGGTGGTGGTTTTATC
+GAGAATGTTCCTCGTATGTTTGCGGATGATTTGGCTGCGGAAATCGATGAGGATAAGGTGCCTGTACTTCCGATTTTCAA
+GGCGCTTGAAAAATATGGTGACATCAAGCACGAAGAAATGTTTGAAATCTTCAACATGGGTGTCGGTCTTATGCTGGATG
+TTAACCCTGAAAATGTTGACCGTGTCAAAGAACTTTTGGACGAACCAGTCTATGAAATCGGTCGTATCATCAAGAAAGCA
+GACGATAGTGTGGTGATTAAATAAGTCACTAAATTTTATAAGAAAGGAGTGTTTAGTTAGTTTGCCTAACTGAACACGGG
+ATTAAATTTCTAGGAAAAAAGATAAAACGACTTAGACGCAAGCGTCGTTGTTCGTTTTCCTATTTTTCTACGAAATTTTT
+CGGCAAGCCGAATCATCCCTTTGTATCGAATATGAAAATCGCTGTTTTTGCTTCTGGTAATGGTTCCAACTTTCAGGTCA
+TAGCAGAGCAGTTTCAAGTTAGTTTTGTCTTTTCAGATCATCGTGATGCCTATGTTTTAGAGCGTGCTCAGAACTTAGCC
+ATTCCAAGCTTCGCTTTTGAACTCAAAGAGTTTGAGAATAAGGCGGCTTACGAGCAAGCCGTCGTTGATTTGTTGGACAA
+ACACGAGATTGACTTGGTCTGTCTGGCGGGCTACATGAAGATTGTCGGAGAAACCTTGCTCTCAGCCTATGAAGGGCGTA
+TCATCAATATTCACCCAACCTATCTGCCTGAATTTCCAGGTGCTCACGGTATCAAGGATGCTTGGGAGGCAGGTGTTGAC
+CAGTCTGGTGTGACCATCCATTGGGTGGACTCTGGTGTGGATACCGGTCAGGTCATCCAACAAGTGCACGTGCCACGCCT
+AGCAGATGATAGTCTAGAAAGCTTTGAAACCCGCATCCACGAAACCGAATACCAACTCTACCCAGCTGTCTTAGATAGCT
+TGGGCATAAAGAGAAAATAGTAAAATTTGTTATAATAAGCTAATGAAACTAGTGAAAAATTTAGAGATAGTAGAGTCTAT
+TTTTGGTGATTGGGACGAGACCATAATCTGGTCGTGTGTCCAAGGTATTATGGGAGAAGTTTTTGTAGATAGTTTAGACC
+AACCAAAATCTTCTTTGGCAAAATTGGGAAGGAAATCATCTTTTGGTTTTCTAGCAGGTCAGCCTACTTTATTTCTACTA
+GAAGTTTGCTCTGGGGAGGATATTATCCTTGTTCCTCAGCATAAAGGATGGTCAGATTTGATTGAATCAACTTATGGTCA
+GAATGCTCATTCTTTTAAGCGTTATGCGACGAAAAAAGATACTTTGTTTGAGCGAAGTAGGTTAGAGAAGTTTGTTACTC
+AGTTGCCAAATGGTTTTGAATTACGTGCTATTGATGAGAAAGTTTACAACTCTTGCTTAGAAAAGGAATGGTCACAGGAT
+TTAGTAGCAAATTACGCTACTTATCAGTACTATAAAAAACAAGGTATAGGTTATGTTGTATATTATCAGGGGAATATCAT
+TGCAGGAGCTTCATCTTATTCAACCTATAAAAATGGGATTGAGATAGAAGTAGATACGCATCCAGATTTTCGTCGGCGTG
+GTTTAGCAACAATAGTTGCAGCTCAGTTAATACTAACTTGTTTAGATAAGGGAATTTATCCTAGCTGGGATGCTCATACA
+AGGACTTCATTGAATTTATCTGAAAAACTCGGTTATGAATTTTCTCATGAATACATAGCCTATGAAATAGATTGAAGTAA
+GAAAAGGAGAACTCATGACTAAACGTGCTTTAATCTCAGTTTCTGACAAATCAGGAATTATTGACTTTGCAAAAGAATTG
+AAAAACTTGGGTTGGGATATTATCTCAACTGGTGGGACTAAGGTTGCCCTTGATGATGCTGGTGTTGAGACCATTGCCAT
+CGACGATGTGACTGGATTCCCAGAAATGATGGACGGTCGTGTTAAGACCCTCCACCCAAACATTCACGGTGGGCTTCTGG
+CTCGTCGCGACGCTGACAGCCACCTTCAGGCTGCTAAGGACAACAATATTGAGTTGATTGACCTCGTGGTTGTCAACCTC
+TATCCCTTCAAGGAGACCATCCTTCGCCCAGACGTGACCTACGATTTGGCGGTGGAAAATATCGACATCGGCGGTCCATC
+AATGCTTCGCTCAGCTGCTAAAAACCACGCTAGCGTAACCGTTGTGGTTGATTCAGCTGACTATGCCACTGTTTTGGGAG
+AATTGGCTGACGCTAGTCAGACGACATTTAAAACTCGTCAACGCTTGGCAGCTAAGGCCTTCCGTCATACGGCAGCCTAC
+GACGCTTTGATTGCTGAGTACTTCACAGCTCAAGTGGGAGAGGCTAAGCCTGAAAAATTGACCATCACTTATGACCTTAA
+ACAGGCTATGCGTTACGGAGAAAATCCACAGCAAGACGCTGATTTCTACCAAAAAGCCTTACCAACAGACTACTCAATCG
+CTTCAGCTAAACAGCTCAATGGAAAAGAATTGTCCTTCAATAATATCCGTGATGCTGATGCAGCAATCCGTATTATCCGC
+GATTTCAAAGACAGTCCAACGGTTGTTGCCCTCAAACACATGAACCCATGTGGTATCGGACAGGCTGATGATATTGAGAC
+AGCTTGGGATTACGCTTATGAAGCTGATCCAGTTTCAATCTTTGGTGGAATTGTTGTCCTTAACCGTGAAGTTGACGCAG
+CGACAGCTGAGAAGATGCACCCTATCTTCTTGGAAATCATCATCGCACCATCATACTCAGAAGAAGCGCTAGCTATTCTC
+ACAAATAAAAAGAAAAACTTGCGTATCCTTGAGTTGCCGTTTGATGCCCAAGCTGCCAGCGAAGTGGAAGCTGAGTACAC
+TGGCGTAGTTGGTGGACTTTTGGTGCAAAACCAAGACGTTGTGGCTGAAAATCCATCTGACTGGCAAGTGGTGACAGACC
+GCCAGCCAACAGAACAAGAGGCGACTGCCCTTGAGTTTGCCTGGAAGGCTATCAAGTATGTTAAGTCTAACGGGATTATT
+ATTACTAACGATCACATGACGCTTGGACTCGGTGCAGGTCAAACCAACCGTGTCGGCTCAGTCAAGATTGCTATCGAGCA
+GGCTAAGGACCACCTTGACGGTGCCGTTCTAGCATCAGATGCCTTCTTCCCATTTGCGGACAACATTGAAGAAATCGCTG
+CCGCAGGGATCAAAGCAATCATCCAACCAGGTGGTTCAGTTCGTGACCAAGAATCTATTGACGCCGCAAACAAACATGGC
+TTGACCATGATCTTCACAGGCGTGAGACATTTTAGACATTAAAAAATAGTAGTTTAGGTTTTCTTAAGTTAACTCAGGTA
+TACTACGTATATCCTAAAAACTTTTCTTTTTATTAAACCTCCTAAGTACTCATCAAGGTGAGTACTTTTTTTGATATTTT
+GATTTAAATTTTCGAATAAGTTAATTGCAAGTGTTTGAGCACTTCATTATATTAATTCTATTTGGAGGTTTTTCTTGAAT
+AAATGGTTAGTTAAGGCAAGTTCCTTAGTTGTTTTAGGTGGTATGGTTTTATCTGCGGGTTCCCGAGTTTTAGCGGATAC
+TTATGTCCGTCCAATTGATAATGGTAGAATTACAACAGGTTTCAATGGTTATCCTGGACATTGTGGGGTGGATTATGCTG
+TTCCGACTGGAACGATTATTAGGGCAGTGGCAGATGGTACTGTGAAATTTGCAGGAGCTGGAGCCAACTTTTCTTGGATG
+ACAGACTTAGCAGGAAATTGTGTCATGATTCAACATGCGGATGGAATGCATAGTGGTTACGCTCATATGTCACGTGTGGT
+GGCTAGGACTGGGGAAAAAGTCAAACAAGGAGATATCATCGGTTACGTAGGAGCAACTGGTATGGCGACGGGACCTCACC
+TTCATTTTGAATTTTTACCAGCTAACCCTAATTTTCAAAATGGTTTCCATGGACGTATCAATCCAACGTCACTAATTGCT
+AATGTTGCGACCTTTAGTGGAAAAACGCAAGCATCAGCTCCAAGCATTAAGCCATTACAATCAGCTCCTGTACAGAATCA
+ATCTAGTAAATTAAAAGTGTATCGAGTAGATGAATTACAAAAGGTTAATGGTGTTTGGTTAGTCAAAAATAACACCCTAA
+CGCCGACTGGGTTTGATTGGAACGATAATGGTATACCAGCATCAGAAATTGATGAGGTTGATGCTAATGGTAATTTGACA
+GCTGACCAGGTTCTTCAAAAAGGTGGTTACTTTATCTTTAATCCTAAAACTCTTAAGACTGTAGAAAAACCCATCCAAGG
+AACAGCTGGTTTAACTTGGGCTAAGACACGCTTTGCTAATGGTAGTTCAGTTTGGCTTCGCGTTGACAACAGTCAAGAAC
+TGCTTTACAAATAGTTTGAGGTATTGATTCATTGTTTTAAATGACAGTTGTGTTACTAACTAAGTACAATTTCTTTAAAC
+CGTCTGAAAATAATTTTATAGTCCAGTAAAGTGTGATATTATAGTCTCGGACTAATAAAAAGGAAATAGGAATTGAAGCA
+ATGAAAATGAATAAAAAGGTACTATTGACATCGACAATGGCAGCTTCGCTATTATCAGTCGCAAGTGTTCAAGCACAAGA
+AACAGATACGACGTGGACAGCACGTACTGTTTCAGAGGTAAAGGCTGATTTGGTAAAGCAAGACAATAAATCATCATATA
+CTGTGAAATATGGTGATACACTAAGCGTTATTTCAGAAGCAATGTCAATTGATATGAATGTCTTAGCAAAAATAAATAAC
+ATTGCAGATATCAATCTTATTTATCCTGAGACAACACTGACAGTAACTTACGATCAGAAGAGTCATACTGCCACTTCAAT
+GAAAATAGAAACACCAGCAACAAATGCTGCTGGTCAAACAACAGCTACTGTGGATTTGAAAACCAATCAAGTTTCTGTTG
+CAGACCAAAAAGTTTCTCTCAATACAATTTCGGAAGGTATGACACCAGAAGCAGCAACAACGATTGTTTCGCCAATGAAG
+ACATATTCTTCTGCGCCAGCTTTGAAATCAAAAGAAGTATTAGCACAAGAGCAAGCTGTTAGTCAAGCAGCAGCTAATGA
+ACAGGTATCACCAGCTCCTGTGAAGTCGATTACTTCAGAAGTTCCAGCAGCTAAAGAGGAAGTTAAACCAACTCAGACGT
+CAGTCAGTCAGTCAACAACAGTATCACCAGCTTCTGTTGCCGCTGAAACACCAGCTCCAGTAGCTAAAGTAGCACCGGTA
+AGAACTGTAGCAGCCCCTAGAGTGGCAAGTGTTAAAGTAGTCACTCCTAAAGTAGAAACTGGTGCATCACCAGAGCATGT
+ATCAGCTCCAGCAGTTCCTGTGACTACGACTTCACCAGCTACAGACAGTAAGTTACAAGCGACTGAAGTTAAGAGCGTTC
+CGGTAGCACAAAAAGCTCCAACAGCAACACCGGTAGCACAACCAGCTTCAACAACAAATGCAGTAGCTGCACATCCTGAA
+AATGCAGGGCTCCAACCTCATGTTGCAGCTTATAAAGAAAAAGTAGCGTCAACTTATGGAGTTAATGAATTCAGTACATA
+CCGTGCGGGAGATCCAGGTGATCATGGTAAAGGTTTAGCAGTTGACTTTATTGTAGGTACTAATCAAGCACTTGGTAATA
+AAGTTGCACAGTACTCTACACAAAATATGGCAGCAAATAACATTTCATATGTTATCTGGCAACAAAAGTTTTACTCAAAT
+ACAAACAGTATTTATGGACCTGCTAATACTTGGAATGCAATGCCAGATCGTGGTGGCGTTACTGCCAACCACTATGACCA
+CGTTCACGTATCATTTAACAAATAATATAAAAAAGGAAGCTATTTGGCTTCTTTTTTATATGCCTTGAATAGACTTTCAA
+GGTTCTTATATAATTTTTATTAAATTGAGGAGATTAAGCTATAAGTCTGAAACTACTTTCACGTTAACCGTGACTAAATC
+AAAACGTTAAAACTAAAATCTAAGTCCGTAAAGATTATTGAAAACGCTTTAAAAATAGATATAATAAGGTTTGTAGATAT
+CTAAAATTAAAAAAGATAAGGAAGTGAGAATATGCCACATCTAAGTAAAGAAGCTTTTAAAAAGCAAATAAAAAATGGCA
+TTATTGTGTCATGTCAAGCTTTGCCCGGGGAGCCTCTTTATACTGAAAGTGGAGGTGTTATGCCTCTTTTAGCTTTGGCA
+GCTCAAGAAGCAGGAGCGGTTGGTATAAGAGCCAATAGTGTCCGCGACATTAAGGAAATTCAAGAGGTTACTAATTTACC
+TATCATCGGCATTATTAAACGTGAATATCCTCCACAAGAACCATTTATCACTGCTACGATGACAGAGGTGGATCAATTAG
+CTAGTTTAGATATTGCAGTAATAGCCTTAGATTGTACACTTAGAGAGCGTCATGATGGTTTGAGTGTAGTTGAGTTTATT
+CAAAAGATAAAAAGGAAATATCCTGAACAGTTGTTAATGGCTGATATAAGTACTTTTGAAGAAGGCAAAAATGCTTTTGA
+AGCAGGAGTTGATTTTGTGGGTACAACTCTATCTGGATACACAGATTACAGCCGCCAAGAAGAAGGACCGGATATAGAAC
+TCCTTAATAAGCTCTGTCAAGCCGGTATAGATGTGATTGCGGAAGGTAAAATTCATACTCCTAAGCAGGCTAATGAAATT
+AATCATATAGGTGTTGCAGGAATTGTAGTTGGTGGTGCTATCACTAGACCAAAAGAAATAGCGGAGCGTTTCATCTCAGG
+ACTTAGTTAAAAGTGTTACTCAAAAATCAAAATCAAAATAAAAAAGGGGAATAGTTATGAGTATCAAAAAAAGTGTGATT
+GGTTTTTGCCTCGGAGCTGCAGCATTATCAATGTTTGCTTGTGTAGACAGTAGTCAATCTGTTATGGCTGCCGAGAAGGA
+TAAAGTCGAAATTACGTGGTGGGCTTTTCCAACCTTTACTCAAGAAAAGGCTAAGGATGGAGTAGGTACTTATGAGAAAA
+AAGTCATCAAGGCTTTTGAAAAGAAAAATCCTAATATAAAAGTAAAACTAGAGACAATTGATTTCACATCTGGACCTGAA
+AAAATCACTACAGCGATTGAAGCAGGGACAGCACCTGATGTGCTTTTTGATGCACCAGGGCGAATTATTCAATATGGTAA
+AAATGGTAAATTAGCAGATTTGAATGATTTATTTACAGACCAATTTATTAAGGATGTCAATAATAAGAATATCATTCAAG
+CTTCTAAGTCTGGCGATAAAGCCTACATGTATCCAATAAGTTCTGCCCCATTTTATATGGCGTTCAATAAAAAAATGCTT
+AAAGATGCAGGAGTTTTGAAACTCGTAAAAGAAGGTTGGACTACTAGTGATTTTGAAAAAGTACTAAAAGCACTAAAAAA
+TAAAGGCTATACACCAGGTTCATTCTTTGCAAACGGGCAAGGAGGAGATCAAGGACCACGTGCATTTTTTGCTAATCTTT
+ATAGTGCTCCAATAACAGATAAAGAAGTAACAAAATATACCACTGACACTAAAAATTCTGTAAAATCAATGAAAAAAATA
+GTTGAATGGATTAAGAAAGGCTACTTGATGAATGGGTCTCAGTATGATGGCTCAGCTGACATTCAAAACTTTGCCAATGG
+ACAAACTGCTTTCACTATCCTATGGGCTCCAGCTCAACCCAAAACTCAAGCAAAATTATTAGAGTCAAGTAAAGTGGATT
+ACCTTGAAGTGCCATTCCCATCAGAAGATGGAAAACCAGATTTAGAATACCTTGTTAATGGTTTTGCGGTCTTTAATAAT
+AAAGATGAAAACAAAGTAAAAGCCTCTAAGAAATTTATCACTTTTATTGCTGACGATAAAAAATGGGGACCAAAAGATGT
+TATACGTACAGGTGCTTTCCCAGTTAGAACATCATTTGGAGATCTTTATAAAGGTGATAAACGTATGATGAAGATTTCAA
+AATGGACTCAATATTATTCACCATATTACAACACTATCGATGGATTTTCTGAAATGAGAACCTTATGGTTCCCAATGGTT
+CAATCTGTATCCAATGGTGACGAAAAACCAGCAGATGCTTTGAAAGACTTTACTCAAAAAGCAAATGATACCATTAAAAA
+AGCAGCTAAATAATTAAGGAGACTCCTTTTCTATGGTCAATCACATATTGGGATAGAAGAGGAGTTTTTAGTCAAGTTAA
+GATGTAAAGGAGAGTACCGTATGCGTACTAATAAGTTAAAGATGAGGGAAACGATGATAGCTTATGCTTTTCTAGCACCT
+ATTCTCTTATTTTTCTTAATTTTTGTTTTTGCACCGATGGTTATGGGCTTTGTCACTAGTTTTTTTAATTATTCTATGAC
+ACAGTTCACTTTTATTGGGTTAGCTAATTACAATCGTATGTTTCATGATTCTATTTTCATGAAATCCTTGATAAATACAG
+TAATCATTGTGATTGGCTCTGTGCCAGTAGTGGTTTTCTTCTCACTTTTTGTTGCTGCCAATACTTATGAAAAAAATGTT
+TTTTCACGCTCTTTCTACCGTTGTGTCTTCTTCTTGCCAGTAGTAACTGGTAGTGTTGCAGTTACAGTTGTTTGGAAATG
+GATTTATGACCCTATGTCCGGAATTTTAAATTACATCTTGAAATCAGGTCATGTCATTGAACAGAATATTAGCTGGCTTG
+GGGATAAGCACTGGGCATTGCTTGCTATTATTATTATTTTGCTAACGACCTCAGTTGGTCAACCTATTATTCTATATATT
+GCGGCGATGGGAAATATTGATAATTCTCTTTGCGAAGCTGCGCGTGTTGATGGAGCCAATGAAATGCAAGTTTTTTGGCA
+AATTAAATGGCCGAGTCTCTTACCAACTACACTCTATATTGCAGTTATAACAACAATTAATTCATTTCAATGTTTTGCCT
+TAATCCAGCTCCTAACATCTGGTGGACCAAATTATTCAACAAGCACTTTGATGTATTATCTTTATGAAAAAGCCTTTAAA
+CTATCAGAATATGGCTATGCTAATACTATGGGAGTATTCCTAGCAGTAATGATTGCTTTAATAAGTTTTGCTCAATTTAA
+GATCTTAGGAAATGATGTGGAATATTAGGAGGAAAACATGAAAAAGAAAACATTCAGTGCTTATAACTTTTTAACGGCTC
+TTATCCTTTGTCTTTTGACAGTGCTTTTTATCTTTCCATTTTATTGGATTATGACAGGAGCTTTTAAATCTCAACCTGAT
+ACTATTATCATCCCCCCACAATGGTGGCCCAAAGCACCGACCTTAGAAAATTTTAAAGCTTTAACTGTACAAAACCCAGC
+TTTGAGATGGCTTTGGAATAGTGTCTTTATCTCAATTATGACAATGTTCCTAGTTTGCTGTACATCGTCAATGGCAGGCT
+ATGTTTTAGCTAAGAAACGATTTTACGGTCAAAAAATATTGTTCTCCCTTTTTATTGCTGCTATGGCTTTACCTAAACAA
+GTTGTTTTAGTGCCATTAGTTAGAATTATCAATTTTATGGGGATACATGATACCTTATGGGCGGTTATTTTACCTCTTGT
+TGGTTGGCCTTTTGGGGTCTTCTTGATGAAACAGTTTTCTGAAAATATTCCAACAGAATTACTGGAATCAGCTAAAATTG
+ATGGTTGTGGAGAGATTCGAACATTTATTAATGTAGCATTTCCAATTGTCAAACCTGGATTTGCTGCCCTAGCTATTTTC
+ACATTTATCAATACTTGGAATGACTATTTTATGCAATTAGTTATGCTAACTTCTAGAAATAATCTGACCATTTCTCTTGG
+GGTAGCTACTATGCAGGCTGAAATGGCAACAAACTATGGCTTAATTATGGCAGGTGCAGCCTTAGCTGCTGTTCCTATTG
+TGACAGTATTCTTAGTTTTCCAAAAATCCTTTACTCAGGGGATTACAATGGGAGCTGTTAAAGGATAGGTAGGATTTATT
+ATGATTTACGATCATTTATTGAATTTAACGCATTATAAAGATATTAATCCTAATTTAGATTTAGCGATTGATTATCTACT
+AAGTCATGATTTAAGGAATTTAGATATAGGCACCTATCATATTAGCCCAGAAGTGATACTCATGGTCCAATCAAATCAAC
+TTAGTGAGTCATTTGATCATATTTTTGAATACCATAAAAAATACCTTGATATACATTATGTCATTGAAGGACATGAAGTT
+ATCAAATTGGGAAAAGGTGATAAGGTAGAGGTGGAGGAATACTTAGGCGATATAGGATTTATCAAGTGCTCAGAAGAGAC
+TTCTTTTGATTTGAGAGATAATTATATAGCCTTCTTTTTCCCAGAAGAAGCTCATCAGCCAAATGGTATGGGAAGTCTAG
+GTAATTATGTCAAAAAAGGGGTATTGAAAGTGTTAATGGCGTAAGAAATACAGGGAGTATATTGTGAAAAAAGCAAATCA
+ATTAATAGCAGCGATTTTTGATGTTAACAACCCCTTTATGCAAGGTTGCAATGTTGTTTTTGATCTGGCATTACTAAACC
+TTCTCTTTATGATAACTTGCCTACCATTGGTAACTATTGGTGCTGCTAAAATTAGTTTGTATCGAACGTTGTGGCAAAAA
+TTAGAAGGTGATCAGACAAATCTTTTAATATTGTATATAAAACACCTAAAAAAAGAGTGGTTCCAAGGTATGCTTTTAGG
+TTTGGTTGAACTAAGTATTTTGGTTGTGATCATATTTGATTTAACAATTCTTCATTATCAAATAGGTTTCATTGTGTCTT
+TCTTGAAGATAACTTGTTACGCCTTTTTGTTATTGACTGTGATGACGAGCATATACCTATTTCCTATGGCTGCCCGCTAC
+GAAATGTCTCTTTTAGATACCGTGAAAAAGAGCTTTATAATGGCATGTTTAAACTTGAAATGGACTGGTGTATTGATGTT
+TTTATTAATCATGACTTGGTTTATTATGGTGCAGTCTAGTCTCTTATTTATGCTTACAGTGTCAGCTATATTTATTTTTG
+CTTATACCGCCTTTGCTTACTTTAAAATTATTATTTTACAAAAACAATTTGCCTATTTCAGCAAACAACAAGGAGATTAT
+CAATGAAAGATTTACAAAAATATCAAGGAATTATTCCTGCATTTTATGCTTGCTATGATGATAAGGGTGATATTTGTCCC
+GAACGAGTAAAAGCCCTGACCAATTATTTTATTGATAAAGGTGTTCAAGGACTTTATGTTAATGGTTCATCCGGAGAATG
+TATTTACCAAAGTGTAGCAGATCGTAAACTTGTACTGGAAAATGTTATGTCCGTTGCTAAGGGTAAACTAACAGTAATAG
+CGCATGTGGCATGTAATAATACTAAGGATAGCGTAGAGTTGGCTATGCATGCTGAAGCTATAGGTGTTGATGCTATTGCA
+GCAATTCCACCAATTTATTTTCGATTACCAGAGTATGCCATAGCAGATTATTGGAATACTATTAGTCAAGCAGCACCACA
+AACTGATTTTATTATTTACAATATTCCTCAATTGGCAGGGGTTGCTTTGACATCGGATTTATATCGAAAAATGTTACAAA
+ATCCGCAAGTAATTGGTGTTAAAAATTCTTCCATGCCAGTTCAAGACATTCAGAATTTTGTGGCTATTGGAGGAGAAAAT
+CATATTGTTTTTAATGGTCCAGATGAACAATTTTTGGGTGGTCGTCTCATGGGAGCCGCTGCAGGTATTGGTGGTACCTA
+TGGCGTAATGCCAGAATTATACTTGACTTTAAATCAGTTAATTGTTGATAAAGATTTAGAAAAAGCGCGTGAACTTCAAT
+TTACAATTAACGATATTATCACAAAGCTTTGTTCGGGTCATGGTAATATGTATGCTGTGATCAAAGCTGTATTGGAAATC
+AATGAGCAACTAACTATAGGTTCCGTTCGGTTACCTTTAGCATCTGTAACAGAAGAAGATAAACCTATTATTAAAGAGGC
+AGCAGAAATGATTAGACATGCTAAAAAACAGTTTTGTTAAAGTGAGGTAGATAATTATGACCAGAACAGTAGCAATTGAT
+ATTGGCGGTACAATGATTAAGCATGGCATTGTGGATAATTTAGGTTGTATTGTTGAGGCAAGTGAGCTTGCCACAGAAGC
+CTACAAAGGTGGTCCAGGCATTTTACAAAAAGTTTGTCAAATTATCGATAACTATCTAGCAGAAGGGAGCATTGATGGAA
+TTGCTATCTCATCTGCTGGCATGGTAGATCCAGATGAAGGATGTATATTTTACTCTGGTCCTCAAATTCCAAACTATGCT
+GGGACACAATTTAAGAAAGTTTTAGAAGACACTTATCAAGTACGCACAGAAATTGAAAATGATGTTAATTGTGCAGGATT
+AGCTGAAGCTGTCTCAGGTAGTGCCAAAGATAGTTCAATAGCGCTTTGTCTTACTATTGGAACAGGTATTGGTGGTTGTC
+TGATTATTGATAAAACAGTTTTTCATGGCTTTAGTAATTCTGCTTGTGAAGTTGGCTATATGCACCTTTCAGATGGTGAT
+TTTCAAGATTTAGCCTCTACAACTGCACTGATTGCTGATGTTGCCAAAGCGCATGGAGATGAAATTAGCCGATGGGATGG
+ACGTCGTATTTTTCAGGAGGCTAAAAAAGGCAATGAAAAATGTATTGCAAGTATAGACCGTATGATAAACTACCTTGGCC
+AAGGAATCGCTAATATGGTTTATGTGGTAAATCCTGAAAAAGTTGTTTTAGGTGGTGGAATCATGGCTCAAAAAGATTAT
+TTACAAGATAAACTTAGTGAATCTTTGAAACGAAATCTTGTGACAAGTCTTGCTGAAAAAACAGCAATAGTCTTTGCACA
+ACACGAAAACCAAGCTGGTATGCTAGGAGCTTACTACCATTTTAAAAACAGGGGGTGACGGGTATATGATTGAAACAATG
+TCGCTAGATGACATGAGAGAATACCTAGGTCAAGACCAAATTCCCGAGGATTTTGATGACTTCTGGAAAAAACAAACAAT
+GAAATATCAAGGGAATATTGAGTATCGTCTAGACAAAAAAGATTTCAATATTACTTTTGCACAAGCTTATGATCTTCATT
+TTAAAGGCAGCAATAACTCTATTGTCTATGCCAAATGTTTATTCCCTAAAACAAATAAACCCTATCCTGTAGTTTTTTAT
+TTTCATGGTTACCAAAACCAAAGTCCTGACTGGAGTGACCAACTTAATTATGTAGCAGCAGGTTACGGCGTTGTTTCAAT
+GGATGTTCGAGGTCAAGCTGGACAGTCTCAAGACAAGGGGCATTTTGATGGCATTACAGTTAAGGGCCAGATTGTGCGAG
+GAATGATCTCAGGACCAAATCATCTTTTTTATAAAGACATTTATCTTGATGTTTTCCAATTGATTGATATCATTGCTACA
+TTAGAGAGTGTTGATAGTAATCAACTTTATAGTTATGGCTGGTCTCAAGGTGGAGCACTTGCTTTGATAGCTGCAGCTCT
+TAATCCCAAAATCGTCAAGACCGTTGCTGTTTACCCATTTTTGTCAGACTTTAGACGAGTATTAGATTTAGGGGGTGTCA
+GTGAGCCCTATGATGAACTCTTCCGCTATTTTAAATATAGTGATCCTTTTCATAAAACAGAGAATAATGTGTTAAAAACT
+TTGGCTTATATTGATGTTAAAAATTTTGCACATAGGATTTCTTGCCCCGTTGTTTTACTAACAGCCTTAAAAGATGATAT
+TTGTCCTCCATCAACTCAATTTGCCATTTTTAATCGTCTGACATCAACTAAAAAGCATCTTTTATTACCAGATTATGGAC
+ATGATCCAATGACAGTGCAAGTAAAAGACCATATTTTTGATCAACTGACAGGAAGTCAATTTACAAAGCAAAAAATCGAG
+TAGATTATTTCTACTCGATTTTCATTTAGCGTTGAATAATGGTTTCTCTAAAAATTCGCTCTTTTTCTATTTTATTAATA
+TCTAAAAATTGTGCATAGATAATATCTACCATGATTAACATTGGGATCTGAGGCGAAATTCTATTGCCGTAGTCTAAATG
+CCTAGCAGAAGCCACCTGAATAATCTTGTCAAAAGCATAGTCAATTGTGTGAGGTTGTTTTGTAAATAGAACGGTTTTAG
+CTCCGTGACAACTTGCGATTTTTAAGGCACCAATAACAGAGTTGGTGTTCCCAGAAAGTGAGAAGGCAATGACGAGGCAT
+CTATCATTAACAATACTATTAGTCCATGAGAAACTATCTGTATCATCCAGAGCCTCACAAATCACTCCCAGCCTCATAAG
+GCGTATTTTAAATTCTTTAGCTACTAGCGATGAGCTCCCTTTGCCATAAAAATAAACACGATCAGCTTGCTCAATCATAT
+GTGATACTTCTAGAAGCTGTTCTTCATCAATAATATCAGCAGATTTAGAAATCATCTCTTGATAATTCATAAATACTTTC
+TTAGTGTTGTCATTTTGAAGACCGTATAATTGTTGACTGATGGTCTCATGGCTTTTTAAATATTCAAAAACAAATTCACG
+ATAGCCTTTAAACCCACATTTTTTAGCAAAACGCGTTAAGGCTGCTTGTGAAATGTGTAGTTGCTTAGTGACAATGGTAG
+AAGCAAGAGCGTCTTTTGAAATGGGCTGCCCCATAAAATAACAAGCAATTTCACGTTCTAAATCAGTCATTAAATCAAGA
+GCAGACTCAATTTGGTCATAAATAGTCATAATACACGGTCCTCTCCTCTTTAAGAAAGCGCTTAATATATTCAGTATAAC
+ATAAAGTTAGTGAGGGACCAAACTAAGTTCTAAGAAACAGCAATGATAAGTTTTAAATAGCAATATGAAGGATCAATAAC
+ATAATATATGTTAAGTATATATTATGATATAAATTTTTCAAAAAAGCTGTAATAAAAAAAATAAAAGCGAACAAATGTGT
+TATAATTTTATAAATGATACGTTTTTATTGAAAATTTCTTTTTATATTATTTAATAGGAGTTATTCTGATATGAAATTGC
+TTGTTGTTGGTTCTGGTGGTCGTGAGCATGCGATTGCTAAGAAGTTGTTAGCGTCTAAGGATGTGGATCAGGTTTTTGTG
+GCACCTGGTAATGATGGTATGACCTTGGATGGTCTAGACTTGGTAAATATCGGAATTTCCGAACATTCTAGACTGATTGA
+CTTTGTTAAGGAGAATGAGATTGCTTGGACCCTTATTGGTCCTGATGATGCGCTAGCAGCTGGTATCGTTGATGGTTTTA
+ATAGTGCTGGACTCAGAGCATTTGGTCCAACCAAGGCAGCCGCGGAGCTAGAGTGGTCAAAAGACTTTGCCAAGGAAATC
+ATGGTCAAATACAATGTTCCAACAGCAGCCTATGGCACATTTTCAGATTTTGAAAAAGCTAAAGCCTACATCGAAGAGCA
+GGGCGCACCAATCGTGGTCAAGGCTGACGGATTGGCGTTAGGCAAGGGCGTGGTCGTGGCTGAAACCGTTGAGCAGGCGG
+TAGAGGCGGCGCAAGAGATGCTTTTGGACAACAAGTTTGGCGACTCGGGTGCGCGCGTGGTTATCGAGGAATTCTTGGAT
+GGTGAAGAGTTCTCCCTTTTCGCCTTCGCTAATGGCGATAAGTTCTACATCATGCCGACAGCTCAGGATCACAAGCGTGC
+CTATGATGGTGACAAGGGGCTAAATACCGGTGGTATGGGTGCCTATGCGCCAGTTCCCCACCTGCCTCAGAGCGTGGTGG
+ATACAGCAGTTGAGACTATCGTTAAGCCTGTCCTTGAAGGCATGATTGCCGAAGGGCGTCCTTATCTAGGTGTCCTCTAT
+GCTGGGCTTATCCTGACGGCTGATGGCCCTAAGGTTATCGAGTTCAACTCACGTTTTGGTGACCCTGAAACTCAGATTAT
+CCTCCCTCGCCTGACTTCCGATTTCGCTCAGAACATCGACGACATCATGATGGGCATCGAGCCTTACATCACTTGGCAGA
+AGGACGGCGTGACTCTGGGCGTTGTCGTTGCCTCAGAAGGCTATCCGCTCGATTACGAGAAAGGTGTGCCACTGCCTGAA
+AAGACCGACGGCGACATCATCACCTACTATGCGGGAGCTAAGTTTGCGGAAAATAGCAAAGCACTGCTCTCAAACGGAGG
+ACGTGTCTACATGCTTGTCACCACAGAAGACAGCGTCAAAGCAGGGCAGGACAAAATCTATACCCAACTCGCCCAACAAG
+ACACAACAGGCCTCTTCTACCGAAACGACATCGGAAGCAAAGCTATTAAGGAATAAGACTACTCATTCAAATATTAGCGT
+CAGCAAAGCGACCGAAGGTCGCTCCAAAAAGAAAGAAGAAAGGAACTGAACACGGGACTAATTTTCTAGTGAAAAAGATA
+AATCTTCCTAGATGCTAAAGCATCTTCGTCAGATTTCTGCGTCGTAGGCGTCTGCTGCTAAAGCACCTAGTCGCCCTGAC
+GTGGGTACGTCTTCGAAATCAAAGATTTCGGACTTACCGCATATTTTTCTACGAAAATTTTCGACAAGTCGAAACGTCCC
+TTTGTATCTTAATATTATGCAACCAATTATTTCTATTATCATGGGTTCCAAATCCGACTGGACAACCATGCAAAAAACGG
+CTGAAGTTCTAGATAACTTTGGCATTGCTTACGAGAAGAAAGTCGTCTCTGCCCACCGTACGCCAGACCTCATGTTCAAG
+CATGCTGAGGAGGCGCGTGGTCGTGGTATCAAGATTATCATCGCTGGAGCAGGTGGAGCAGCCCACTTGCCGGGTATGGT
+AGCAGCTAAAACAACCCTGCCTGTTATCGGTGTGCCTGTCAAATCACGTGCCCTCTCAGGTTTGGATTCGCTCTACTCTA
+TTGTGCAGATGCCTGGTGGTGTGCCTGTGGCGACCATGGCTATCGGAGAAGCAGGAGCGACTAACGCTGCCCTGACAGCC
+CTCCGTATCCTCTCTATCGAGGATCAAAATCTGGCTGATGCGCTAGCTCATTTCCATGAGGAACAAGGAAAAATCGCAGA
+GGAGTCAAGCAATGAACTCATTTAAGACCATTGGGATTATTGGTGGTGGTCAGCTGGGGCAGATGATGGCGATTGCGGCT
+ATCTACATGGGCCACAAGGTCATTACGCTGGATCCAGCTAGCGACTGCCCTGCCTCCCGCGTTAGCGAGGTGATTGTGGC
+ACCTTACGATGATGTTGAGGCTTTGGGAACATTAGCTGCGCGTTGCGATGTTTTGACCTATGAGTTTGAGAATGTCGATG
+CCGATGGTCTGGATGCCGTTGTGTCAGCTGGTCAGCTACCGCAGGGGACTGATCTGCTCCGCATTTCTCAAAACCGTATC
+TTTGAAAAAGACTTTCTGGCAAATAAGGCTGGCGTGACTGTCGCTCCCTATAAGGTGGTGACATCTAGCCTTGACCTAGA
+GGGGCTTGACTTGACCAAGACCTATGTCCTCAAGACAGCGACAGGTGGTTATGACGGTCATGGGCAAAAGGTTATCCGCT
+CAGCAGAAGACCTGCCAGAGGCGCAGCAATTAGCCAACTCAGCTCAGTGTGTCTTGGAAGAGTTTGTCAACTTCGACCTT
+GAAATATCAGTCATCGTGTCTGGAAATGGTCAGGATGTGACGGTCTTTCCCGTTCAGGAAAATATCCACCGCAACAATAT
+CCTGTCAAAAACCATCGTACCAGCTCGCATCTCAGACCAACTAGCTGACAAGGCTAAGGAAATGGCTGTGCAGATTGCCA
+AGAAACTCCAGCTATCAGGAACCCTCTGTGTGGAAATGTTTGCGACCGCAGATGACATCATCGTCAATGAAATTGCCCCA
+CGTCCCCACAACTCAGGGCACTACTCTATCGAAGCCTGCGACTTTTCACAGTTTGACACCCACATCTTGGGCGTACTGGG
+CGCACCGCTTCCGCCAATCAAACTCCATGCTCCAGCCGTTATGTTCAATGTCCTAGGACAACATGTCCAGCAGGCAATTG
+ACCATGTTGCCCAAAACCCTAGCGCCCACCTCCACATGTATGGTAAACTAGAAGCAAAACATAACCGCAAAATGGGACAC
+GTGACGGTGTTTAGCGATGTACCTGATGAGGTGGAAGAGTTTGAAGAAAGGATGGATTTCTAAGGAGGTTTATGGAATTT
+TAGGGGGGAGAATGATTTTGAAGGGAGTGTTGTCAGATGAATAGAATAATAAACAGGGATATTTTACCTAGAATTTCAAA
+GATTTCTAAAAATAATAAAGAGAAAGATTTACTATCTATAGCTTATATTACTTGGCTAATCTTTATAATATTTGCTTTGG
+GAGTAGTTACAGTTAATGATTTAAAACCGATGTTTAATCAATTAATAGTAAACCTCTTAAATATTTATTATTATATGGAA
+GCCTTCATATTGGGTATGGACAGCTATTTACAATATAACCTTCCATACAGTTTTGATTTTTGGAGTATTTTTGTAGAGGC
+TATAAATTTATTTGTAAAAGTATTTTTAATTGCTTTTATTCCTTCTGTTATTAGAAAAGTATTGAAAAAAGAAAGTTTTT
+TCAATGAAGTTGTTATTTTACTAGGAGCGATTGTTACTATAATTGTAAGTTTCCATTTATATTTAGAGATATTGATAGTA
+GTGGGACTAATACTTTTATTAATTGCTTTTGTTTCAATAGGTAAGAATCGTGTTTATAATTTTGTTCAAAATTTAAACTA
+CTTTGAAGAAGTGATTTGGAATTATTTTGAAGAAAATCCGGTTAAAATAAAAGAAAAATCATTGATTATTAAATTTTTAC
+TTACTATTTCTTTTGTTTTTGTAATTGATTTTGCAATGGTTAGATTGTTGAATTTTAATATAAAATTTTCTACAATATTA
+GCTTGTTCTGCTATTTTATTAGCATGGTTATACCAAAATAAGTCTGTTACAGAACCCTTCCTATTAAAAAAGTTAGTTAT
+CTATTTTATTTTTTTCATTGCCACTTTAATTGGTAATTTAAAAAATGAGTTGTCAATCTTAGAAACACCATTACTTTTTA
+TTAGTATATTTTTTACTATGGATAGAATTATTGCTCTATCTAAAGAAATGCGTGATTTGATTATATCTAAGAGTATTTTA
+TTTTATTATGATCATGAAAATATAAAGCCATCAATATTACTTAGTGAGATAAAAGAAATTAAGTATCTTGAAAATGTAGA
+TATTGGAGAACTTGAACTTGTTAGGCAAATGGTAATTAGGTTGCGTCTAGAGTTAGAGGAAGAATTTTTGATTTTATCAG
+ATATATATATGAAAAATGGCTATGAAAAATATATACAATTTGTTCAAGGAAATGTTTATTTTATCAACTTAGAATTGGAT
+AAAATTCCCAACTACACTAACTTGAAATTAATACTAGAATCAATATTTGATCATAATAATCAAAAGATATTTATACCTAA
+ACTTTATGAGGAATACATATACATCTTAATTTCTTTAGGAGAAGTTGAAAAAGCTAAAGAAATATTAAAAGAAGTGTCGG
+ATTATTTAACTGAAGAATCTTTGAATTATTTTGAAAAAGAATATGATAAAGCTAAGGGTAGTAATTAGAATTTTTTAAAG
+GAGTAAAACAAAATGATCGAACGTTATTCACGCCCTGAGATGGCGGCAATTTGGACAGAGGAAAATAAATACCGTGCTTG
+GTTGGAGGTCGAGATTTTGGCTGACGAGGCATGGGCTGAGTTGGGTGAGATTCCTAAGGAGGATGTGGCTAAGATTCGTG
+AGAAGGCGGATTTTGACATTGACCGCATTCTTGAGATTGAGCAGGACACGCGTCACGATGTGGTGGCTTTCACTCGTGCG
+GTTTCTGAGACGCTTGGTGAGGAGCGCAAGTGGGTGCACTACGGTTTGACGTCGACTGACGTGGTGGACACTGCCTACGG
+TTACCTCTACAAGCAGGCTAACGATATTATCCGTCGTGACCTTGAGAATTTCACAAATATTGTGGCTGATAAGGCTAAGG
+AGCACAAGTTCACCATCATGATGGGTCGTACCCACGGTGTTCACGCTGAGCCAACGACTTTCGGTCTTAAGTTGGCGACC
+TGGTACAGCGAGATGAAACGTAATATTGAGCGTTTTGAACATGCTGCCGCAGGTGTGGAAGCTGGTAAGATTTCAGGTGC
+CGTTGGTAACTTTGCTAACATTCCTCCATTTGTGGAACAATATGTTTGTGACAAATTGGGCATCCGTCCGCAAGAGATTT
+CAACACAGGTTCTTCCACGTGACCTCCACGCAGAATATTTTGCAGTGCTTGCAAGCATTGCAACTTCTATCGAACGTATG
+GCGACAGAGATTCGTGGTCTGCAAAAATCAGAACAACGTGAAGTTGAAGAATTCTTTGCCAAAGGTCAGAAAGGTAGCTC
+TGCTATGCCTCACAAACGCAACCCAATCGGTTCAGAGAACATGACTGGGCTAGCGCGCGTGATTCGTGGTCACATGGTGA
+CGGCTTATGAGAACGTGGCACTTTGGCACGAGCGTGATATTTCGCACTCATCTGCTGAGCGTATCATCACACCTGACACA
+ACGATCTTGATTGACTACATGCTCAACCGTTTTGGCAATATCGTTAAGAACTTGACTGTCTTCCCGGAAAATATGATGCG
+CAATATGGAATCAACTTTTGGTTTGATTTATAGTCAACGTGTTATGCTCAAATTGATTGAAAAAGGAATGACACGAGAAG
+AAGCTTATGACTTAGTTCAACCTAAGACAGCTTATTCCTGGGACAATCAAGTGGATTTCAAACCACTTTTAGAAGAAGAC
+ACCAAAGTTACCTCTTGTCTTACACAGGAAGAAATTGATGAACTATTTAATCCGATTTATTACACAAAACGTGTTGATGA
+TATTTTTGAAAGACTAGGATTAGAAAAATAAGAAAATTCCATTACTGGTTAACGTTTTTTTAACCAGTAATGGAATTTTT
+ATTGATTTAAAAGGAATTAATATTAAAAAACATACTTAAAATGAGTTTATTATGATAATATATAATAAGAAGAAAAATTT
+AGGAGTTAGTTTTTAAAGGAAAATGTTAAAACATTTTGGTAGTAAAGTAAGAAATTTGAGAGTAACTAGAAATATTACTC
+GCGAAGATTTTTGTGGTGATGAAACTGAGTTATCTGTAAGACAATTAGCTAGGATTGAAAGTGGACAGTCAATTCCAAAC
+TTGACTAAAGCTCACTACATAGCTAAACAATTGAATGTAAAATTGGATATTTTAACAGGAGGAGAGAGCTTAGAATTACC
+TAAACGGTATAAAGAGTTGAAGTATTTGATTTTAAGAATTCCAACTTATGCAGATGCTGAACGATTAAAATTAAGAGAAT
+GTCAGTTTGATCATATTTTCGAAGAATTCTATGATAATCTTCCAGAAGACGAGTGCTTAGCAATTGACAGTTTACAAGCT
+AAATTTGAAGTCTATCAAACAGGAGACATTAATTTTGGTGTGGAGGTTTTATGCGAATGCTTTGATAAAGTAAAATATAA
+AGAAAAATATACTCTTAATGATTTGATTATCATAGATTTGTTTTTAACTTGTGCAGTTGTATCTAAATTTAACAATAGAG
+CATTTACTAAAGAAGTATTTCAAACTATATGTAAAACTTTGATAAGTCAGAACCACAAACTTACAGCAGAAGATTTGTTT
+TGGTTTAATCATGTACTCCTGAATTGTGTATTTGTTGGACTTTGTTTAAATAGTGAAGAGTGTCTTGCAGAAATGTTAGA
+AGTTAGCCGACAAACGATGGTGTCAACACATGATTTTCATAAAATGCCTTTATATTTTATGTACCAATGGAAATACTTCA
+TTACAATTGACAATGATATAAAGTCTGCAGAAAATGCTTACCAACAATCAATTATGTTTTCAAAAATGATTGATGACAAG
+CATCTAATTAAAAAATTAGAATTGGAGTGGCAAGAAGATATAACAGGACATTGATGTCCTGTGACTCTGAGGTCTAAAAA
+TTTATAATAAACGTACAAAATATTATTTAGGAGTTTATTATAGTGATTAAAAAATGTTTTTTAATAGTATTACTTGTTCT
+ATTATCAAATTTAGGTTCATTTGATTTGTTTTTAGGAATGGGTTGGTGGAATATGGGCTAAGTAAGCTGTTCTGTGATTT
+CTTGAGGTTGGATTAACTATAAGATCAGTTTATTCTTCCTTTAAATAAGGGAGATACTAATACACCAACTTAGTTCTTAA
+CTTTTCCTATACAAATGTTATAATAATATCATGACAAGATTTTTAGATAGTGATGCAATGGGTGACGAAGAATTGGTAGA
+ACGTACACTTCGTCCGCAGTATTTAAGAGAGTATATTGGACAAGATAAGGTTAAAGATCAGCTAAAAATATTTATTGAAG
+CTGCTAAATTGCGTGATGAGTCATTGGATCATGTGTTATTATTTGGCCCTCCTGGTTTAGGGAAAACAACCATGGCATTT
+GTAATTGCTAATGAGTTGGGTGTCAATCTCAAACAAACATCAGGTCCCGCAATTGAAAAATCAGGGGATTTAGTAGCCAT
+TTTAAATGATTTAGAACCAGGTGATGTTCTTTTTATTGATGAAATTCATCGTATGCCGATGGCGGTTGAAGAGGTACTTT
+ATAGTGCAATGGAAGACTTCTATATTGACATTATGATCGGTGCAGGAGAAACTAGTAGAAGTGTTCATCTAGATTTGCCG
+CCCTTTACCTTAATTGGTGCAACGACACGTGCAGGTATGTTATCTAATCCCTTACGTGCTCGCTTTGGTATTACAGGGCA
+TATGGAGTATTATGAAGAAAATGATTTGACAGAAATTATTGAGCGTACAGCAGACATTTTTGAAATGAAAATTACTTATG
+AAGCTGCTTCTGAATTAGCGCGTCGCAGTCGTGGAACGCCACGTATCGCTAACCGTTTATTGAAACGTGTTCGAGATTAT
+GCTCAAATCATGGGAGATGGTTTGATAGATGACAATATTACAGATAAAGCATTAACGATGTTAGATGTTGATCACGAGGG
+GCTTGATTACGTCGATCAAAAAATCTTAAGAACCATGATTGAAATGTATAATGGAGGTCCTGTTGGTTTAGGAACTCTAT
+CCGTTAATATTGCTGAAGAACGAGATACTGTTGAAGACATGTACGAACCTTATTTAATTCAAAAAGGTTTTATTATGCGT
+ACCCGTACCGGTCGTGTAGCTACGGTTAAGGCATATGAACATTTAGGTTATCAGCGATTTGATAAATAAAACATAAGTCA
+TTTTAAGGCTAGAGTATCTAGTCTTAATTTTTTAATTTTCATGCAATGTTAAGTATTAGATATGTTGTAGTTATTCTTTG
+AGCAGTTAAACGTATTATAAGTACCTTTTTTCTGTTATAATAGACCAAAAGGAGTTTGCTATGAAGAAAGTCTGTTTTGT
+TTGTCTTGGAAATATCTGCCGTAGCCCGATGGCTGAGTTTGTTATGGCGAATTTAGATAAGGAGGATAGCCTCTTGGTTG
+AGAGTCGTGCGACTTCAACATGGGAGCATGGAAATCCTATACATAGGGGAACGCAAGCGATTTTGCAGCGTTATCAAATT
+CCTTACATTAACGATAAAGGGTCACAACCTATTTCTAAAGACGATTTAGCATATTTTGATTATATCATCGGTATGGATGA
+GCAAAATGTCAAGGATTTAAAAGCTCTATCACAAGGAACCTATGATGATAAGATTAGTCTTTTTTGTGATGGTGGTGTTC
+CTGATCCATGGTATACTGGTGATTTTGAGGAAACCTATCGTCTAGTCAATGATGGCTGTAAACAGTGGTTAACGCTAATA
+AATAATAGTAGAGATTAAGTAGAAATGAAGAATTTTAAAATAACACGAACTCATCTAGAAATATTATCTTTGATAATTAT
+TGTTGTTTTTGGTTTATCAGTATTTACCTTAACGACTTCTAGTCAAGGAGTCTTTAGCTATGATGGCGGCAAGATAAAAT
+ATGTGGGCTCTATTGTTAATCACCATATGACTGGTAAAGGTAAATTAACCTATGAGAATGGGGATTACTATAAGGGCGAT
+TTTGTAAATGGAGTCTTTGAAGGGAAAGGAACATTTGTTTCAGTTCATGGCTGGTCTTATACAGGTGACTTTAAAAAAGG
+TCAACCTGATGGACAAGGTCGCCTCAATGCTAAAAATAAGAAAGTCTATAAGGGGACATTTAAACAGGGGATTTATCAAA
+AATGAGAATAAAATGGTTTTCTTTGGTACGTATAACAGGACTACTACTTGTTTTACTTTACCATTTCTTTAAGAATAGTT
+TTCCAGGAGGATTTGTTGGCGTTGACATCTTCTTTACATTTTCTGGTTTTCTGATTACGGCCTTATTGATTGATGAATTT
+TCTAAAACGAAAAAAATTGATTTTGTTAGTTTTTGTCGTAGACGTTTTTACCGTATTTTCCCACCATTAGTATTGATGGT
+TTTGGTGACAATACCTTTTGTATTTCTGGTTAAAAGCGATTTTAGAGCAAGTATTGGCTCTCAAATTATGACTGCTTTAG
+GTTTTACCAGCAACTTTTACGAAATCTTGACTGGTGGTAACTACGAAAGTCAATTTATCCCTCACTTATTTGTGCATACC
+TGGAGTCTTTCTATTGAAGTCCATTTTTATGTTTTATGGGGCTTAACGGTATGGCTCTTATCGAAAAGATCAAAAGATCA
+AAAGCAATTGAGGGGGACTTTGTTCCTTATTTCCATGGGAATTTTTGGAGTCAGCTTCCTTACCATGTTTGTTAGAGCCT
+TTTTCGTTGATAATTTTTCAACGATATATTTCTCTACATTATCACATATATTTCCGTTCTTTTTAGGAGCGATGGTGGCT
+ACAATATCTGGTATTCGAGAGATTACCGGACGATTCAAGAAAAATATCAAAAATCTGACTTTGAAGCATAATTTAATCAT
+GATGGGTAGTGCTTTTGCTGGTCTAATGATTTTAACTTTTGCACTTGATTTTGATAATCGGCTAACATATCTTTTTGGTT
+TTGTATTGTCTAGCATTTTTGCTAGTGTAATGATTTACAATGCACGTATTTTACACGAGCATACACCAGATATTTCAGAA
+CCTTTTGTGATTACTTATCTTGCTGATATCAGTTACGGTATGTACCTTTTTCATTGGCCATTTTATATTATTTTTAGTCG
+TTTATCCCCAAACTGGATAGCTGTTATTTTGACAGTAGTATTATCAGCAGTCTTCTCAACATTATCATTTTATATCATTG
+AACCTTTTATTTTAGGTAGAAAACCTAAATTCCTTGATTATGAATTTGACTTGTTGCCTTACAAAAAGTGGTTATTTAGT
+ATCGGAGGGGTACTAACTCTTATTACTGTAGTGACAATGTTGACAGCTCCAAGTATAGGTAGTTTTGAGACAGAATTATT
+GCAGAATTCGTTACAACAAGCTAGAACAAATACTAACCGAACACATACACTAGCCGCAGGGGATGCAGGTGCTCTTAGTG
+ATGTGACAGTAATCGGAGATTCAGTTGCCTTAAGGTCAAGTGCTGCTTTTAATAAATTGTTACCAGAAGTACAATTAGAT
+GCTGCGGTGAGTCGTAATTTTAGTAAATCATTTGATATTTTTGAAAACCGTATTCAAAATAAAGCCTTGTCCAAAATTGT
+TGTTTTGGCAGTTGGTGTGAATTCATTAGATAACTACAAGACAGACTTGAGCCAATTTATTAAATCTTTGCCTAAGGGAC
+ACCGTTTGATTATAGTAACACCTTATAATGCTAAAAATATGAGTCAAGTTACGACAGTGCGTGATTATGAACTCTCGCTA
+ATGAAAAAATATAATTACATAACGGTTGCTGACTGGTATAAGGTTGCGACAGAACATCCAGAAATCTGGGGAAATACAGA
+TGGTGTGCATTATAGTGATAGCGATACTACAGGGGCTGATTTATATGTTAGTAACGTCAAAAAAGCTATTCAAAAATCAG
+CTCAACGAGCTGCAAAATAAACAAGTCCGAGTCATGTACTCGGCTTTTTTTGTGAAAACGAATAATAGATATCTCCGTTT
+ATGGTGATAAAAATGAAATCGATAGGCTTTAATCTGAAAATTAGTAATGAAAAAACAAATATAATTAAAGCGCTTTCAAG
+AAATATTTCCGAAAGATTGAAAAAAAGTTCACAAAAAAGTTGTGAAACTATTTACAAAGTTTTTAAATATGCTATAATAA
+TCTCGTAAACAAATTTGTGAAACATTTAACAAATCAAAAGGAGTCTCAAATGACTGAAAAAACTAAAGCAGTAGAAACTA
+CAGATGTTGCTCTTGCAATTGATACATTGGTTCAAAATGGTTTAAAAGCACTTGATGAGATGCGTCAACTTAATCAAGAA
+CAAGTTGATTATATTGTAGCTAAAGCTTCTGTTGCAGCCTTGGATGCCCATGGAGAACTTGCTCTTCATGCAGTAGAAGA
+AACTGGTCGTGGTGTCTTTGAAGATAAAGCGACAAAAAATTTATTTGCATGTGAACACGTCGTTAACAACATGCGTCATA
+CAAAGACAGTGGGAGTTATTGAAGAAGACGATGTCACAGGCTTGACATTAATTGCTGAACCAGTGGGAGTTGTCTGTGGT
+ATCACGCCAACAACCAACCCAACTTCAACTGCTATTTTCAAGTCATTAATCTCTCTTAAAACACGTAATCCAATTATTTT
+TGCCTTCCACCCATCAGCACAAGAATCATCAGCACATGCAGCACGTATTGTTCGTGATGCTGCTATTGCTGCTGGAGCTC
+CTGAAAATTGTGTCCAATGGATTGAACAACCATCAATTGATGCAACTAATGCTTTGATGAACCATGATGGTATTGCCACT
+ATCCTTGCGACAGGTGGTAATGCGATGGTTAAAGCTGCCTACTCATGTGGGAAACCTGCCCTTGGTGTAGGTGCTGGGAA
+TGTTCCAGCTTATGTTGAAAAATCAGCTAATATCCGACAAGCCGCTCACGATATTGTTATGTCTAAATCATTTGATAACG
+GTATGGTATGTGCATCAGAACAGGCTGTTATTATTGATAAAGAAATTTATAAAGAATTTGTTGAAGAATTTAAATCTTAT
+CATACCTATTTCGTTAATAAGAAAGAAAAAGCTCTTCTTGAAGAATTCTGTTTTGGTGCAAAAGCAAATAGCAAAAACTG
+TGCTGGTGCAAAATTAAATCCAAATATTGTTGGAAAATCAGCAGTTTGGATTGCTGAACAAGCTGGATTTACTGTTCCAG
+AAGGAACAAATATTCTTGCCGCAGAATGTACTGAAGTTAGTGAAAAAGAACCTTTGACACGTGAAAAACTATCACCTGTT
+ATTGCAGTATTGAAAGCTGAATCTACAGAAGATGGTGTTGAAAAAGCTCGTCAAATGGTTGAGTTTAATGGTCTAGGGCA
+CTCAGCTGCTATTCATACAAAAGATGCAGACTTAGCTCGTGAATTTGGAACTAGAATTCGTGCTATCCGTGTTATTTGGA
+ATTCTCCTTCTACTTTTGGTGGTATTGGGGATGTTTACAATGCTTTCTTGCCATCATTGACTCTTGGTTGTGGTTCGTAT
+GGACGTAACTCAGTTGGTGATAACGTTAGTGCTATAAATCTCTTGAATATCAAAAAAGTAGGAAGACGTAGAAATAATAT
+GCAATGGTTTAAAGTCCCTTCAAAAACATACTTCGAACGTGATTCTATTCAATATTTGCAAAAATGTCGCGATGTTGAAC
+GTGTCATGATTGTTACAGATCACGCCATGGTTGAGCTTGGTTTCTTGGATCGTATCATTGAACAACTTGATCTTCGTCGC
+AATAAAGTTGTTTATCAGATTTTTGCTGAAGTAGAACCAGATCCAGACATTACAACAGTAATGAAAGGAACAGATTTGAT
+GCGTACCTTCAAACCAGACACTATTATTGCATTAGGTGGTGGTTCTCCTATGGATGCTGCGAAAGTTATGTGGCTCTTCT
+ATGAACAACCAGAAGTTGATTTCCATGACCTCGTTCAAAAATTCATGGATATCCGTAAACGTGCGTTCAAATTCCCAGAA
+CTTGGTAAGAAAACAAAATTTGTTGCTATTCCAACAACTTCTGGAACAGGTTCTGAAGTGACACCATTTGCCGTTATCTC
+TGACAAAGCAAATAATCGTAAATATCCAATCGCTGATTATTCATTAACACCAACTGTAGCTATCGTTGATCCGGCCCTTG
+TTATGACTGTTCCTGGTTTTATTGCGGCTGATACGGGTATGGATGTATTGACACATGCAACAGAGGCTTATGTTTCACAG
+ATGGCAAATGATTATACAGACGGACTTGCTCTTCAAGCAATTAAAATTGTGTTTGACTACTTAGAACGCTCAGTAAAAGA
+TGCTGATTTTGAAGCACGTGAAAAGATGCACAATGCGTCAACTATGGCAGGTATGGCTTTCGCCAATGCATTCTTAGGTA
+TTTCTCACTCAATGGCGCATAAAATTGGCGCACAATTCCATACCGTACACGGACGTACAAATGCAATTCTTTTGCCGTAT
+GTTATCCGCTATAATGGAACTCGTCCAGCTAAAACAGCAACATGGCCTAAGTACAATTACTATCGTGCTGACGAAAAGTA
+TCAAGATATCGCTAAATTACTCGGCTTACCAGCAGCAACACCAGAAGAAGCTGTCGAATCATATGCAAAAGCTGTGTATG
+ACCTTGGAACACGTTTAGGTATTAAGATGAATTTCCGCGACCAAGGCATTGATGAAAAAGAATGGAAAGAAAAATCTCGT
+GAACTAGCTTTCTTAGCATATGAAGATCAATGTTCACCAGCAAATCCACGCCTTCCGATGGTAGATCACATGCAAGAAAT
+CATCGAAGATGCTTATTATGGTTATGAGGAACGTCCAGGACGTCGTAAGTAACAGCAGTCGAAGAATCTCACTCTATTGA
+GTGGGATTTTTAGTTTCAAAAAGATTAACCGGTTAAGAATATTTTCAAAAAATTTTCTGAAAATCACTTGACATAGTTTG
+TGAAGAATAATACAATATAAAATGTAAACGATTACAAAATAAGATATATTTATTTCTAGGAGGTTTTATCATGAAAGCGG
+TTGTTGTTAATCAAGCTAGTACAGGTGTTGAAGTTGTTGAGCATGATCTTCCAAAAGTTGGTCATGGTGAAGCACTTGTA
+AAAGTAGAATACTGTGGTGTATGCCATACTGATTTACACGTTGCACATGGAGATTTCGGCCAGGTACCAGGACGCATTTT
+GGGTCACGAAGGCATTGGTATAGTAGAAGAAATTGGAGAAGGCGTAACGTCTTTGAGGGTTGGTGATCGTGTCTCTATTG
+CATGGTTCTTTGAAGGGTGCGGTCATTGCGAATACTGTACTACAGGACGTGAGACACTTTGTCGTAGTGTTAAAAATGCT
+GGATACAGTGTTGATGGTGGTATGAGTGAATACGCTATTGTTACCGCGGACTATGCGGTTAAGGTTCCTGAGGGATTAGA
+CCCAGCTCAAGCATCATCAATCACTTGTGCTGGAGTAACAACATACAAGGCTATCAAAGAAGCTGGAGCTGCTCCTGGTC
+AGTGGATTGCAGTGTATGGTGCAGGTGGTCTTGGAAACTTAGCAGTCCAATATGCAAAAAAAGTATTCAATGCTCATGTT
+GTAGCTGTTGATATTAACGCAGATAAACTTCAATTAGCTAAAGAGGTTGGAGCAGATTTGACAGTTAATGGCAAAGAAAT
+AAAAGATGTTGCGGCATATATTCAAGAAAAGACAGGCGGTTGTCATGGAGTGGTTGTGACTGCTGTTTCTAAAGTTGCGT
+TTAATCAGGCGATTGACAGCGTTCGTGCTGGAGGTACAGTGGTAGCTGTCGGTCTTCCATCAGAATATATGGAATTGAGT
+ATTGTAAAAACAGTACTTGATGGGATTCGTGTGGTTGGTTCCTTAGTTGGAACTCGTAAAGACTTAGAAGAAGCCTTCGC
+ATTTGGAGCAGAAGGCTTGGTAGTACCGGTGGTTGAAAAAGTGCCTGTGGATACAGCTCCTCAAGTATTCGATGAAATGG
+AAAGAGGATTGATTCAAGGACGTAAAGTTCTTGACTTTACAAAGTGATAATGATGTTACGAACCCCCTTTATTTTAATAA
+AGGGGGTTAATTATATAACGAACAATGGACATGTTATTAAATTGTGTTACAATAACTAAAAGATATTTATATAAAGAGGG
+ATTCTTATGGCAATAGTATATCAATCAACACGTGATGCTAGTAATAAAGTGACAGCTAGTCAAGCGATTCTAAAGGGATT
+AGCTGACGATGGAGGACTCTTTACCCCCATCACATTTCCAAAAGTTGATTTAGATTTCACTAAACTTAAGGATGCTTCCT
+ACCAAGAAGTGGCTAAACTCGTTTTGTCAGCTTTTTTTGATGATTTTACTGAACAAGAATTGGATTACTGTATTAGTCAA
+GCTTATGATACTAAATTTGATACAACTGAAATAGCCCCGATAGTAAAGATTGGAGACCGGTATCACCTTGAATTATTTCA
+CGGTCCTACAATTGCATTTAAAGATATGGCTTTATCCATTCTTCCTTATTTGCTAACAACAGCAGCCAAAAAACAAGGGG
+TTGATAATAAAATCGTTATTTTAACAGCAACATCAGGTGACACTGGCAAGGCAGCGATGGCAGGTTTTGCAGATGTTCCA
+GGAACTGAGATTATTGTCTTTTATCCTAAAAATGGTGTTAGTTATATCCAAGAATTGCAGATGATAACACAAGCCGGACA
+AAATACTCATGTTGTTGCGATTGAAGGAAATTTTGATGATGCACAGACTTCAGTTAAAGAAATGTTCAATAATTCCCTTC
+TTCGATTAAAATTATCACAGCAGCATATGCAGTTATCATCAGCCAATTCAATGAACATCGGTCGCCTTGTTCCTCAAATT
+GTTTACTATATATATGCATATGCTCAATTAGTTAAGTCAAAGGAAATCTCAATTGGTCAACCAATTAATTTTAGTGTACC
+TACAGGAAATTTTGGTAATATTTTAGCAGCATATTATGCTAGTCAAATTGGATTACCTGTTACCAAACTCATTTGTGCCT
+CAAATGATAATAACGTTCTAACAGATTTTTTTAAGACACAAACCTACGATAAAAATCGAGAATTTAAAGTGACATCAAGT
+CCCTCTATGGATATTTTGGTCTCCTCTAATCTAGAACGATTAATCTTTCACCTTTTAGGCGATGATGCAGAAACGACTAA
+AAAATTAATGGAAGATTTAGTGACTACTGGGGAGTATGCCTTAGAGGCTAGGCAAGCAAATATTTTAGAGAGCTTTGTAG
+CGGGATTTGCGACAGAACAATTTGTTGAATTAGACATCAAACATTTATTTGACCAGTATCAGTATATAGAGGATCCGCAT
+ACAGCTGTAGCATCAGCTGTTTATCAAGCTTATCAGACAGAAACTAAAGATCAAACTCCAGCAGTAATTGTGTCAACAGC
+AAGTCCTTATAAGTTCCCGTGTGTTGTTACAAAGGCTATTACAAATAAAGAAGAGATACAGGATTTCGCTGCTATTTCAA
+TCTTAAACGATTTGTCAGGTGTTTCTTTACCTAAGGCGGTTACAGATCTACAAAAGGCCGAAGTAATCCATAGAACGGTA
+GTACCTACCTCAAATATGCGAGAAACGGTTGAAGAGTGTCTAGGTTTGAAACAATAATAAAAATACGATTGTTTTAAAAT
+ATTTAGAGCGAGAAAGAAACATTTTAGAAATTTTCCCATCACTCTCTTTTTAATGATCCTGGGTAATAGAAAGGAGATAC
+TGTGCGTTATAGTAAAGAGATTATTCAGTTAGCTATACCAGCTATGATTGAAAATATCTTACAAATGCTCATGGGAGTAG
+TTGATAATTATCTAGTGGCTCAGTTAGGTGTTGTAGCAGTATCAGGTGTTTCAGTTGCTAATAATATAATTACTATTTAT
+CAAGCTATTTTTATAGCTTTAGGGGCGAGTATAGCAAGTCTATTGGCCAAGTCGTTAGCAGGTAGTAAGAAGGATGATGC
+AATTTCAGTATGTTCTCAAGCCATTTTTCTAACATTACTGATAGGGGCAGTATTAGGAATTATCTCGATTGTTTTTGGAC
+AAACTTTCTTTAAACTTTTAGGGACAACAAAAAGTGTCGCACAAGTTGGTGGTTTATATTTAGCAATTGTGGGTGGAGGT
+GTTGTTACTTTAGGAATGTTAACCACCCTAGGCTCATTTTTACGTGTGCAAGGGCAACCTCGTTTACCAATGTATGTCAG
+TATTTTTGTCAATTTCCTCAATGCAGTCTTATCAGGTTTTGCTATTTTTGAGTGGCGCTATGGTTTGGTCGGAGTGGCAG
+TATCAACTCTTATCGCAAGATTAATTGGTATTTGTATCCTTGCGAAGTATCTTCCTATTAAAAAGATAATAAAAAGAATG
+ACTTGGAAAATCAGTGCACAAATTTGGAATCTTGCCTTACCATCAGCAGGAGAACGTCTGATGATGCGAGCTGGAGATGT
+TGTTATAGTTGCTATTGTTGTTCAGTTAGGTACAAATGTTGTAGCGGGAAATGCTATTGGAGAAACCTTGACACAATTTA
+ATTATATGCCAGGACTTGGCATCGCAACTGCTACAATTATCCTAACTGCAAAATATGTAGGACAAAAAAACAGAGAATCT
+ATAGAAGAAACTATTCAAAGTTCGTATTATATTGGCTTAGTTCTAATGATCCTTATATCAAGTTTTATGCTTCTTGCAGG
+CAAACCATTGACACAGTTATTTACAAATAATCCTTCTGCCATTAAAGGAAGTTTGATTGTTATTTTGCTATCTTTCGTAG
+GAGTACCTGCTACTATTGGGACCTTGGTTTATACAGCAGCTTGGCAAGGATTAGGAAATGCTAAACTCCCATTTTACACA
+ACGACTATAGGCATGTGGTTAATCAGAGTAGTTCTTGGTTATTTATTAGGAATAGTTTTTGAATTAGGTTTGCTTGGGGT
+TTGGATGGCTACGATAGCAGACAATATCTTTAGGTGGCTGTTTTTGAAAGTTCACTATCATCGATATATTCAAAAAATGT
+AACCAGAAATGGTTGCATTTTTTTCGAAAATAATAAAATAATGCTTGCGTGTGCTGTTTTTTTTTGATATCATATACTGG
+TGCTGTGTATGAACAGCTTTAGCTATGATGCAAGAGGTTGCGACACGCTAGGTTGCATTGCCACGCGACTCGTGTTGGTT
+TTCTTGAGGAGCTAGCCTATTATCGTAAATAGACGAGAGGAGAAAAGATGGCAAACAAAAAAATCCGTATCCGTTTGAAA
+GCGTACGAACACCGTACACTTGATACAGCGGCAGAAAAAATCGTTGAAACTGCAACACGTACAGGTGCTACAGTTGCTGG
+ACCAGTTCCGCTTCCAACTGAACGCAGTCTTTACACAATTATTCGTGCGACTCACAAATATAAAGATTCTCGCGAACAGT
+TTGAAATGCGTACACACAAACGTTTGGTAGACATCATCAACCCAACACAAAAAACTGTTGATGCTTTGATGAAACTTGAT
+CTTCCAAGTGGTGTCAACGTAGAAATCAAACTTTAATTTGATTTCTGAGCACAAAAAACGCTCGTAAAAAACTTTTTTGA
+GCACAAAAAACGCTCATAAAAAACTTTTTGAAATAAAATAAGAAAAGGAAATATTTTCTCATGACAAAAGGAATCTTAGG
+GAAAAAAGTGGGAATGACTCAAATCTTCACTGAATCAGGCGAATTCATCCCTGTTACTGTCATTGAAGCAACTCCAAACG
+TTGTGCTTCAAGTTAAAACTGTTGAAACAGACGGTTACGAAGCAGTTCAGGTTGGTTTTGATGACAAACGTGAAGTATTG
+AGTAACAAACCTGCCAAAGGCCATGTTGCAAAAGCAAACACAGCTCCTAAGCGCTTCATTCGTGAATTCAAAAACATTGA
+AGGCTTAGAAGTTGGTGCAGAATTATCTGTAGAACAATTTGAAGCTGGTGATGTTGTTGACGTCACAGGGACATCAAAAG
+GTAAAGGTTTCCAAGGTGTTATCAAACGCCATGGTCAATCACGTGGTCCTATGGCTCACGGTTCTCGTTACCATCGTCGT
+CCAGGTTCTATGGGACCTGTTGCGCCTAACCGCGTTTTCAAAAACAAACGCTTGGCAGGACGTATGGGTGGTAACCGTGT
+AACAGTTCAAAACCTTGAAATTGTACAAGTTATCCCAGAGAAAAACGTTGTCCTCATCAAAGGTAACGTACCAGGTGCTA
+AGAAATCTCTTATCACTATCAAATCAGCAGTTAAAGCTGCTAAATAATAAGAAAGGAGAAAACAGTTAAAATGGCAAACG
+TTAAACTATTTGACCAAACTGGTAAAGAAGTTAGCTCAGTTGAGCTTAACGAAGCTATCTTCGGTATTGAACCAAACGAA
+TCAGTTGTTTTTGATGTTGTAATCAGCCAACGCGCTAGCCTTCGCCAAGGAACTCACGCGGTTAAAAACCGTTCAGCAGT
+ATCTGGTGGTGGACGTAAACCATGGCGTCAAAAAGGAACTGGACGCGCTCGTCAAGGTTCTATCCGCTCACCACAATGGC
+GTGGTGGTGGTGTTGTCTTTGGACCAACTCCACGTTCATACGGCTACAAACTTCCACAAAAAGTTCGTCGCCTTGCGTTG
+AAATCAGTTTATTCAGCAAAAGTTGCTGAAGATAAATTTGTAGCTGTAGAAAACCTTTCATTTGCAGCTCCAAAAACTGC
+TGAATTTGCGTCAGTTCTTTCAGCACTTAGCATTGATTCAAAAGTACTTGTAATCCTTGAAGAAGGTAACGAATTTGCTG
+CACTTTCAGCGCGTAACCTTCCAAACGTTACAGTTGCTACTGCAACTACTGCAAGTGTTCTTGATATCGTTAACGCAGAC
+AAACTTCTTGTTACTAAAGAAGCAATCTCTACAATCGAGGGGGTTCTTGCATAATGAATTTGTATGACGTAATCAAAAAA
+CCTGTTATCACTGAGAAATCAATGGTTGCTCTTGAAGCAGGGAAATATACATTTGAAGTTGACACACGTGCACACAAACT
+TTTGATCAAACAAGCTGTTGAAGCTGCATTTGACGGAGTAAAAGTTGCAAGTGTAAACACTGTGACAGTTAAACCCAAAG
+CAAAACGTGTTGGTCGTTACACAGGTTTCACTTCAAAAACTAAAAAAGCTATTATCACTCTTACAGCTGATTCAAAAGCA
+ATCGAGTTGTTTGCTGCTGAAGCTGAATAATCTAAGGAGGAAATAACGTGGGTATTAAAGTTTATAAACCAACGACAAAT
+GGCCGTCGTAATATGACTTCTTTGGATTTTGCAGAAATCACTACAAACACTCCTGAGAAATCATTGCTTGTTTCACTAAA
+GAATAAAGCAGGACGTAACAACAACGGACGTATTACTGTTCGTCACCAAGGTGGTGGACACAAACGTCATTACCGTTTGA
+TTGACTTCAAACGTAATAAAGATGGTGTTGAAGCAGTTGTTAAAACAATTGAATACGATCCAAATCGTACTGCAAATATT
+GCTCTTGTACACTATACTGATGGTGTTAAAGCTTACATCCTTGCGCCTAAAGGCCTTGAAGTAGGTCAACGCATTATTTC
+TGGTCCAGAAGCAGACATCAAAGTTGGTAACGCACTTCCGCTTGCTAACATTCCAGTCGGTACAGTTATCCATAATATTG
+AATTGCAACCAGGTAAAGGTGCTGAATTGATTCGTGCCGCTGGTGCTTCTGCTCAAGTACTTGGTCAAGAAGGTAAATAT
+GTTCTTGTTCGCCTTCAATCAGGTGAAGTACGTATGATCCTTGGTACTTGCCGTGCAACAATTGGTACTGTTGGTAATGA
+ACAGCAATCACTTGTTAACATTGGTAAAGCAGGACGTAATCGTTGGAAAGGTGTTCGCCCTACAGTTCGTGGTTCTGTAA
+TGAACCCTAACGATCACCCACACGGTGGTGGTGAAGGTAAAGCACCAGTTGGTCGTAAAGCACCATCTACTCCATGGGGT
+AAACCTGCGCTTGGACTTAAAACTCGTAATAAGAAAGCTAAATCAGACAAACTTATTGTTCGTCGTCGTAACCAAAAATA
+ATAGGTTAATAGCATAATCTTATACAAATCCGCCAGCTCGGTAGTACACTATAGTGTACAGGCCGTTGTGGTACATTATT
+TAAAGGAGAAAACTACAAAATGGGACGTAGTCTTAAAAAAGGACCTTTCGTCGACGAGCATTTAATGAAAAAAGTTGAAG
+CTCAAGCAAATGACGAAAAGAAAAAAGTAATCAAAACTTGGTCACGTCGTTCAACGATTTTCCCAAGTTTCATCGGATAC
+ACAATCGCAGTTTATGATGGACGTAAACATGTTCCTGTTTATATCCAAGAGGACATGGTAGGTCACAAACTTGGTGAATT
+TGCACCAACACGTACTTACAAAGGTCACGCAGCTGACGACAAGAAAACACGTCGTTAATAGGAGGAGGACACAATGGCAG
+AAATTACTTCAGCTAAAGCAATGGCTCGTACAGTGCGTGTTTCACCTCGTAAAACACGTTTAGTACTTGATCTTATCCGT
+GGTAAGAATGTTGCTGACGCAATCGCAATCTTAAAATTCACTCCAAACAAAGCAGCTCGTGTTATTGAGAAAACTCTTAA
+CTCAGCAATTGCAAATGCAGAAAACAACTTTGGTTTGGAAAAAGCAAACTTGGTAGTATCTGAAACATTCGCTAACGAAG
+GACCAACAATGAAACGTTTCCGTCCACGTGCGAAAGGTTCAGCTTCACCAATCAACAAACGTACAACTCACGTAACTGTA
+GTTGTATCAGAAAAATAAGGAGGTAAAATCGTGGGTCAAAAAGTACATCCAATTGGTATGCGTGTCGGAATCATCCGTGA
+CTGGGATGCGAAATGGTATGCTGAAAAAGAATACGCGGATTACCTTCATGAAGATCTTGCAATCCGTAAATTCATTAATA
+AAGAATTAGCTGACGCATCAGTTTCAACTATTGAAATTGAACGTGCAGTAAACAAAGTTATTGTTTCACTTCACACTGCT
+AAACCAGGTATGGTTATCGGTAAAGGTGGAGCAAACGTTGACGCTCTTCGTGGTCAACTTAACAAATTAACTGGAAAACA
+AGTACACATCAACATCATTGAAATCAAACAACCTGATTTAGATGCTCACCTTGTTGGTGAAAATATTGCTCGTCAATTAG
+AGCAACGTGTTGCTTTCCGTCGTGCTCAAAAACAAGCAATCCAACGTACAATGCGTGCAGGAGCTAAAGGTATTAAAACT
+CAAGTTTCTGGTCGTTTGAACGGTGCTGATATCGCTCGTGCTGAAGGTTATTCAGAAGGAACTGTTCCGCTTCACACGCT
+TCGTGCTGATATCGACTATGCTTGGGAAGAAGCTGACACAACTTATGGTAAACTTGGCGTTAAAGTTTGGATTTACCGTG
+GAGAAGTTCTTCCAGCTCGTAAAAACACTAAAGGAGGCAAATAACAAATGTTAGTACCTAAACGTGTTAAACACCGTCGC
+GAATTCCGTGGAAAAATGCGCGGTGAGGCTAAAGGTGGTAAAGAAGTTTCATTCGGTGAATACGGACTTCAAGCTACAAC
+TAGCCACTGGATTACAAACCGTCAAATCGAAGCTGCCCGTATTGCGATGACTCGTTACATGAAACGTGGTGGTAAAGTTT
+GGATTAAAATCTTCCCACACAAATCATACACTGCAAAAGCTATCGGTGTACGTATGGGTTCTGGTAAAGGGGCACCTGAA
+GGTTGGGTAGCACCAGTTAAACGTGGTAAAGTGATGTTTGAAATTGCTGGTGTTTCTGAAGAAGTTGCACGTGAAGCATT
+ACGTCTTGCTAGCCACAAATTACCAGTTAAATGCAAATTCGTAAAACGTGAAGCAGAATAAGGAGAAGACATGAAACTTC
+AAGAAATTAAAGATTTTGTTAAAGAGCTTCGTGGATTGTCTCAAGAAGAACTTGCTAAGAAAGAAAACGAACTCAAAAAA
+GAATTGTTTGATCTTCGTTTCCAAGCTGCAGCAGGTCAACTTGAAAAGACTGCTCGCCTTGACGAAGTTAAGAAACAAAT
+TGCACGTGTTAAAACTGTGCAATCAGAAATGAAATAATAGATTGGGAAAGGAGAAATTCTAAATGGAACGTAATCAACGT
+AAAACTCTTTACGGACGCGTAGTGTCTGACAAGATGGACAAAACAATCACAGTTGTAGTTGAAACTAAACGTAACCACCC
+AGTCTATGGTAAACGTATCAACTATTCTAAAAAATATAAAGCACATGATGAAAACAACGTTGCTAAAGAAGGCGATATCG
+TTCGTATCATGGAAACTCGCCCACTTTCAGCTACAAAACGTTTCCGTCTTGTGGAAGTAGTGGAAAAAGCTGTTATTATC
+TAATCAAACTAAAAGGAGAAAATTGAAATGATTCAACAAGAAACTCGCTTGAAAGTTGCTGATAATAGCGGTGCTCGTGA
+GATCTTGACTATCAAAGTACTTGGTGGTTCAGGACGTAAATTCGCTAACATCGGTGACGTAATCGTTGCTTCTGTAAAAC
+AAGCTACTCCTGGTGGAGCAGTTAAAAAAGGTGATGTGGTTAAAGCTGTTATCGTTCGTACAAAAACTGGTGCACGCCGC
+CCAGACGGTTCATACATCAAATTTGACGACAATGCTGCTGTAATCATCCGTGACGATAAAACTCCTCGCGGAACTCGTAT
+CTTTGGCCCAGTTGCACGTGAATTGCGTGAAGGTGGCTACATGAAGATCGTTTCATTGGCACCAGAAGTACTTTAATCTC
+AGATTAACAAACGTAGTCCCCTAGGATTTCCTAGGGTGCCTTTCGAGGCGTAAGAAAAATAGGAGAAAAACTCAAATGTT
+TGTAAAAAAAGGCGACAAAGTTCGCGTTATTGCTGGTAAGGACAAAGGCACTGAAGCTGTAGTTCTTAAAGCTCTTCCAA
+AAGTAAACAAAGTTGTTGTTGAAGGCGTAGCCCTCATCAAGAAACATCAAAAACCAAATAACGAAAACCCTCAAGGCGCT
+ATCGTTGAAAAAGAAGCTCCAATCCATGTGTCAAACGTTCAAGTTCTTGATAAAAATGGTGTAGCAGGACGTGTTGGTTA
+CAAAGTTGTTGACGGCAAAAAAGTTCGTTACAACAAAAAATCAGGCGAAGTGCTTGATTAATCACGAAGGAAAGGAGAAG
+CATAATGGCAAATCGCTTAAAAGAAAAATATACTAATGAAGTTGTTCCTGCGTTGACAGAAAAATTTAACTATTCATCTG
+TTATGGCTGTGCCAAAAGTTGAGAAAATCGTTCTTAACATGGGTGTTGGTGATGCTGTATCAAACGCTAAAAATCTTGAG
+AAAGCTGCTGCTGAGTTAGCACTTATTTCAGGTCAAAAACCACTTATTACTAAAGCTAAGAAATCAATCGCTGGCTTCCG
+TCTTCGTGAAGGTGTAGCGATCGGTGCAAAAGTTACCCTGCGCGGTGAACGTATGTACGAATTCTTGGATAAATTAGTTT
+CTGTTTCACTTCCACGTGTACGTGACTTCCATGGTGTTCCAACGAAATCATTTGATGGACGTGGAAACTACACTCTTGGA
+GTTAAAGAACAATTGATCTTCCCAGAAATCAACTTTGATGACGTTGATAAAGTACGTGGTCTTGATATCGTTATCGTTAC
+TACTGCTAACACTGATGAAGAGTCACGTGAATTGCTAAAAGGCCTTGGAATGCCTTTTGCAAAGTAATCTAGGAGGTAAA
+TAAATTGGCTAAAAAATCTATGATTGCTAAGAACAAACGCCCAGCGAAGTTCTCTACGCAAGCTTACACTCGTTGTGAAA
+AATGCGGACGTCCACACTCAGTTTACCGCAAATTCCAACTTTGCCGTGTTTGCTTCCGTGACTTGGCTTATAAAGGTCAA
+GTACCAGGCGTAACTAAAGCATCTTGGTAATAAATTAATGATGCTTTGTGTTTAAAAGGTGTCGTTGATAATGGCACTGA
+TTTTTAAACGCAAATATACTAAGACCTAGTCTTACAACGTCCGTAAGGACTCATTAATTAGCAAGTGATTCAATTCAAAC
+TGCTAATAAGAGGAGAATTAAAAAATGGTTATGACTGACCCAATTGCAGACTTTTTAACTCGTATTCGTAATGCTAACCA
+AGCAAAACATGAAGTGTTAGAAGTACCTGCATCAAACATTAAAAAAGGGATTGCTGATATCCTTAAACGTGAAGGTTTTG
+TAAAAAACGTTGAAGTTATTGAAGATGACAAACAAGGCATCATCCGTGTGTTCCTTAAATATGGACAAAATGGTGAACGT
+GTTATCACTAACTTGAAACGTATTTCAAAACCAGGTCTTCGTGTTTATACTAAACATGAAGATATGCCTAAAGTTCTTAA
+CGGACTTGGTATTGCAATTGTATCAACTTCTGAAGGTCTTTTGACTGACAAAGAAGCTCGCCAAAAAAATATTGGTGGAG
+AAGTACTTGCATATATTTGGTAAAATTTTACCTAAAATGCTCATTGAGTCACAGTATAATCCTGTGTTCTCATGAGTCCC
+CGTGAAAACTAGTTGCTCAAGCAGCTTGACAATTTAACAGGAGAAAATAAACATGTCACGTATTGGTAATAAAGTAATTA
+CATTGCCTGCAGGTGTTGAAATCATTAACAAGGATAATGTTGTTACTGTAAAAGGACCTAAAGGCCAACTCACTCGTGAG
+TTTAATAAAAATATTGGAATCACTGTTGAAGGGACTGAAGTAACAGTTACTCGTCCTAACGACTCAAAAGAAATGAAAAC
+AATTCATGGTACAACTCGTGCGAACTTGAACAACATGGTTGTTGGTGTTTCTGAAGGTTTCAAAAAAGCTCTTGAAATGC
+GCGGTGTTGGTTACCGTGCACAACTTCAAGGATCAAAACTTGTTCTTTCTGTTGGTAAGTCTCACCAAGACGAAGTTGAA
+GCTCCAGAAGGTGTTACTTTTGAAGTGCCAACTCCAACAACAATCAACGTAATCGGTATCAACAAAGAAAGCGTTGGACA
+AACTGCTGCTTACGTTCGTAGCTTACGTTCACCAGAACCATATAAAGGTAAAGGTATTCGTTACGTTGGTGAATTCGTAC
+GCCGTAAAGAAGGTAAAACAGGTAAATAATAGGATTGATAGATTTTGTAGAATCTTTTCTGCAAATTCTCTATCTTTTCA
+TTTTAATATTGTCATTTTGACATAACAATATATTTAAGAGGTGAAAATTGTGATTTCGAAACCAGATAAAAATAAAATCC
+GCCAAAAACGCCACCGTCGTGTTCGCGGTAAACTCTCTGGAACTGCTGATCGCCCACGTTTGAACATTTTCCGTTCTAAT
+ACAGGCATCTACGCTCAAGTAATTGATGACGTAGCGGGTGTAACGCTCGCAAGTGCATCAACTCTTGATAAAGAAGTTTC
+TAACGGAACAAAAACAGAACAAGCCGTTGTTGTCGGTAAACTTGTTGCTGAACGCGCAGTAGCTAAAGGTATTTCTGAAG
+TGGTGTTTGACCGCGGTGGATATCTCTATCACGGACGTGTAAAAGCTTTGGCTGACTCAGCTCGTGAAAACGGATTGAAA
+TTCTAATAGGGAGGACACTTAATAATGGCATTTAAAGATAATGCAGTAGAACTTGAAGAGCGCGTTGTTGCGATTAACCG
+CGTTACAAAAGTTGTTAAAGGTGGACGTCGTCTACGTTTTGCAGCTCTTGTAGTTGTTGGTGACCGTAATGGTCGTGTTG
+GTTTTGGTACAGGTAAAGCTCAAGAAGTACCAGAAGCTATTCGCAAAGCTGTTGAAGCTGCTAAGAAAAACATGGTTGAA
+GTTCCTATGGTCGGTACAACAATTCCTCACGAAGTTCGTTCAGAATTTGGTGGAGCGAAAGTATTGTTGAAACCAGCTGT
+TGAGGGTGCTGGGGTTGCCGCTGGGGGTGCTGTTCGTGCCGTCATCGAATTAGCAGGTGTTGCAGATATTACATCTAAAT
+CACTTGGTTCAAACACTCCAATCAACATTGTTCGCGCAACTGTTGAGGGCTTGAAACAATTAAAACGTGCAGAAGAAGTT
+GCTGCTTTACGTGGCATTTCTGTTTCTGACTTAGCATAAGAAAGGGGATTATAATGGCTCAAATTAAAATTACTTTGACT
+AAGTCTCCAATCGGTCGCAAACCAGAACAACGTAAAACAGTTGTTGCCCTTGGACTTGGTAAATTAAACTCTTCAGTTGT
+TAAGGAAGATAATGCTGCCATCCGTGGTATGGTTAACGCTATCTCTCACTTAGTAACTGTTGAAGAAGCTTAATTAAATG
+CTAAATCGCACTGATTGTTATTGGTGCGATTTAAACAAATCGTATAGGCGAGTCTTTGCGGGGAGTACCTTTTCCCTCGT
+AAAGGCGTTAGCATTTTACAAATAAGGAGAAAAAATAATGAAACTTCATGAATTAAAACCTGCAGAAGGATCACGTAAAG
+TCCGCAATCGTGTGGGTCGCGGTACATCTTCAGGTAATGGTAAAACTTCTGGACGTGGTCAAAAAGGACAAAAAGCGCGT
+AGTGGTGGTGGAGTACGCCTTGGTTTTGAAGGTGGACAAACTCCATTGTTCCGTCGTATGCCAAAACGTGGGTTCTCAAA
+CATCAATGCAAAAGAATATGCTCTTGTGAACCTTGACCAATTAAATGTCTTTGAAGATGGTACTGAAGTAACTCCAGTTG
+TTCTTAAAGAAGCTGGAATCGTGCGTGCTGAAAAATCAGGCGTTAAAATTCTTGGTAATGGTGAATTAACTAAGAAATTG
+TCTGTTAAAGCAGCTAAATTTTCTAAATCTGCTGAAGCAGCTATCACTGCTAAAGGTGGTTCAATCGAAGTCATCTAATT
+AATGAGAGGTAACTCATTATGTTTTTAAAATTACTTAGAGATGCACTCAAAGTAAAGATGGTAAGAAATAAAATTTTATT
+TACTATCTTTATCCTTCTTGTATTTCGTATCGGAACGCATATCACAGTACCGGGCATCAATGTTAAGAGTTTAGAACAAA
+TGGGTGAACTTCCATTTCTAAATATGCTTAACTTAGTTAGTGGTAATGCAATGAGAAACTTTTCGGTATTCTCTATGGGA
+GTTAGCCCTTACATTACTGCGTCTATTGTTGTTCAGTTACTTCAAATGGATATTCTTCCGAAGTTTGTTGAATGGGGAAA
+ACAAGGAGAGGTAGGTCGTCGTAAGCTTAACCAAGCTACACGTTATATTTCTTTGTTCCTTGCATTCGTACAATCAATTG
+GTATTACTGCTGGTTTTAACACTCTATCAAGTGTTGCTTTAGTTAAAACTCCGAATGTACAAACATATTTGCTTATTGGT
+GCAATCCTTACAACAGGTAGTATGGTGGTTACTTGGCTAGGTGAACAAATTACTGATAAGGGATTCGGAAATGGAGTGTC
+TATGATTATCTTTGCGGGTATCATTTCTTCCATTCCAAGTGCAATTACAACTATCTACGAAGATTTCTTTGTAAATGTAC
+GCTCTTCAGCAATTACAAATTCTTACATCTTTGTCGGGATCCTTATCGTAGCAGTATTAGCAATTGTATTTTTTACAACA
+TTTATTCAACAAGCTGAATACAAAATTCCAATCCAATATACAAAACTTGTTCAAGGAGCTCCTACAAGTTCATATCTTCC
+TCTAAAAGTAAATCCAGCTGGTGTTATTCCCGTTATCTTTGCTAGCTCGATTACAACAATTCCAAGTACGATTATTCCTT
+TCTTTCAAAATGGCAAAGAAATTCCTTGGCTTACTAAACTCCAAGAATTACTTAATTATCAAACCCCAGTCGGTATGATT
+ATCTATGCTATCTTGATTATTCTGTTCTCTTTCTTCTATACTTTTGTACAAGTAAACCCTGAAAAGACAGCAGAGAATCT
+TCAAAAAAATTCGTCCTACATTCCAAGTATTCGACCAGGACGAGAAACAGAAGAATATATGTCATCGCTATTGAAAAAAT
+TAGCAACAATTGGTTCAGTATTTCTAGCATTTATTTCCTTGTTACCAATTATTGCTCAACAAGCGTTGCATTTGTCATCA
+AGTATTGCGTTAGGTGGGACAAGCTTACTCATTTTGATTGCAACGGGTATTGAAGGTATGAAACAACTCGAGGGCTATCT
+TTTGAAGAGACGCTATGTTGGATTCATGAATACAACAGAATAGAATATAGGTTGACTCTGTCAACCTTCTATTTTGTTTT
+TTAATAAGTCCGACATGCTGTGTTGGATTTATTTAAAAACAAAATAAGGAGACTATAATGAATCTTTTAATTATGGGTTT
+GCCTGGTGCTGGTAAAGGTACTCAAGCAGCTAAGATCGTTGAAGAATTTGGTGTTGCTCACATCTCAACAGGGGATATGT
+TCCGCGCCGCAATGGCTAATCAAACCGAAATGGGACGTTTAGCTAAAAGTTATATTGATAAAGGTGAATTGGTTCCTGAT
+GAAGTAACAAACGGGATTGTAAAAGAGCGCTTAGCTGAGGATGATATCGCAGAAAAAGGTTTTTTACTTGATGGATATCC
+ACGTACTATTGAACAAGCACACGCCTTAGATGCTACGCTTGAAGAACTAGGACTACGCTTAGATGGTGTTATTAATATTA
+AAGTGGATCCATCATGTCTTATAGAGCGTTTGAGTGGTCGTATTATCAATCGTAAAACTGGTGAAACTTTCCACAAAGTG
+TTCAACCCACCAGTAGATTATAAAGAAGAAGATTACTATCAACGTGAAGATGATAAGCCTGAAACTGTCAAACGTCGCTT
+GGACGTTAATATTGCTCAAGGAGAACCTATTCTTGAACACTATCGTAAGCTTGGTCTTGTTACAGATATTGAAGGTAATC
+AAGAAATAACAGAAGTTTTTGCAGATGTTGAAAAAGCGTTGCTAGAACTCAAATAAATTATGCTAATCTACTTGCATAAG
+TAGATTAGTAATGATATACTAAGTTAGTCTGACTTATAATTGTTACCTCTTTATAGAGGACATCAAATCGAAATTTAGGG
+GGTACTTTTGCGTGGCAAAAGAAGATGTGATTGAAATTGAAGGTAAAGTTGTTGAAACTATGCCTAACGCAATGTTTACT
+GTTGAGTTGGAAAATGGACACCAAATTTTGGCAACTGTATCAGGAAAAATCCGTAAAAACTACATCCGTATTTTGGTAGG
+TGATCGTGTTACTGTTGAAATGAGCCCATACGATTTAACACGTGGACGCATCACATACCGCTTTAAATAGTCGAAATAAT
+TGGAGGGATTAAAACATGAAGGTAAGACCATCGGTTAAACCAATTTGCGAATACTGTAAAGTTATTCGTCGTAACGGTCG
+TGTTATGGTAATTTGTCCGACAAACCCAAAACACAAACAACGTCAAGGATAATATAGAAAGGAGATAAAATGGCTCGTAT
+TGCTGGAGTTGATATTCCAAATGACAAACGTGTAGTAATTTCACTTACTTATGTATACGGAATTGGTCTTTCTACATCTA
+AAAAAATCTTAGCAGCTGCAGGTATTTCTGAAGATATCCGCGTTAAAGATTTGACACCAGATCAAGAGGACGCTATCCGT
+CGTGAAGTTGATGCAATCAAAGTTGAAGGTGACCTACGTCGTGAGGTAAACTTGAATATTAAACGTTTGATGGAAATCGG
+TTCATACCGTGGAATCCGTCACCGTCGTGGACTTCCTGTCCGTGGACAAAATACTAAAAATAACGCTCGCACTCGTAAAG
+GTAAAGCTGTTGCGATTGCAGGTAAGAAAAAATAAAATAGGAGGTAAAACAATTGGCTAAACCAACACGCAAACGTCGTG
+TGAAAAAGAACATCGAATCTGGTGTTGCTCATATTCACGCTACATTCAATAACACTATTGTTATGATTACAGATGTGCAT
+GGTAACGCTCTTGCATGGTCATCAGCTGGTGCTCTTGGATTTAAAGGTTCTCGTAAATCTACTCCATTTGCTGCTCAAAT
+GGCTGCTGAAGCTGCTGCTAAATCTGCACAAGAACACGGTCTTAAAACTGTTGAAGTTACTGTAAAAGGTCCTGGTTCAG
+GTCGTGAATCTGCTATCCGTGCCCTTGCTGCAGCTGGTCTTGAAGTAACTGCAATTCGTGATGTGACTCCTGTACCACAT
+AATGGTGCTCGTCCTCCAAAACGTCGTCGTGTATAATCATAGCATTTTATAGTACACAACTTTTCGTTTAAGAGGGAGTA
+ACTAAATGATTGAGTTTGAAAAACCAATAATAACAAAAATTGATGAAAATAAAGATTACGGCAGATTTGTCATCGAACCA
+CTAGAACGTGGCTACGGTACAACTCTAGGAAACTCTCTTCGTCGTGTGCTTCTGTCTTCACTTCCAGGTGCAGCAGTCAC
+ATCAATCAAAATTGATGGAGTATTACACGAATTTGATACTATCCCAGGTGTACGTGAAGATGTGATGCAAATCATCCTTA
+ATGTAAAAGGACTTGCTGTGAAATCTTACGTCGAAGACGAAAAGATTATCGAACTAGACGTTGAAGGTCCTGCAGAAATT
+ACTGCCGGAGATATTTTAACAGATAGTGATATCGAAATTGTAAACCCTGACCATTATCTTTTCACAATTGCTGAAGGTCA
+CAGTTTGAAAGCAACAATGACAGTTGCTAAAAACCGAGGTTATGTTCCAGCAGAAGGAAATAAAAAAGATGATGCACCAG
+TGGGAACATTGGCTGTAGATTCAATCTATACACCAGTGAAAAAAGTTAATTATCAAGTTGAACCTGCTCGTGTAGGTAGT
+AACGATGGCTTTGATAAATTAACTATTGAAATCATGACAAATGGCACAATCATTCCTGAGGATGCTCTTGGTCTTTCAGC
+TCGCGTCTTAATTGAACACTTAAACTTGTTTACTGATTTAACAGAGGTTGCTAAAGCAACTGAAGTAATGAAGGAAACAG
+AGAAAGTGAACGATGAGAAAGTGCTTGACCGGACAATTGAGGAACTTGATTTGTCAGTGCGCTCATATAACTGTTTAAAA
+CGTGCTGGAATTAATACAGTATTTGATTTAACAGAAAAAACTGAGCCTGAAATGATGAAAGTCCGAAACTTAGGACGTAA
+GAGTCTTGAAGAAGTTAAAATCAAACTTGCCGATCTAGGTCTTGGATTAAAAAACGATAAATAAAATAGGAGGACATAAT
+GGCTTACCGTAAACTAGGACGCACTAGCTCACAACGTAAGGCAATGCTTCGTGATTTGACAACCGATCTTCTTATCAACG
+AATCAATTGTAACTACTGAAGCACGTGCTAAAGAAATCCGTAAAACAGTTGAAAAAATGATTACTCTAGGTAAACGTGGT
+GATTTACATGCTCGTCGTCAAGCTGCTGCTTATGTACGTAATGAAATTGCATCAGAAAACTATGATGAAGCTTCTGATAA
+ATATACATCAACAACAGCTCTTCAAAAACTTTTTGACGACATCGCACCTCGTTATGCTGAACGTAACGGAGGATACACTC
+GTATTCTTAAAACAGAACCACGCCGTGGCGATGCTGCCCCAATGGCAATTATTGAATTAGTATAATTTTTATCAATTTTG
+TTGAGTGTTATGATGATGGAATCAATCGATTCTTAGTCTAGCTCTGGTCTACCGCTGAGAATTATTCTCAGCGGGAACAC
+TCATCATATATTGTTAAATAGGTAACGCTTGTTTACGAAATGCAAACAATTTTGTTTATATTTCGTAAGCAGGCGTTTTA
+TGCATTATTATATTTATTGGATATTTTCGATGAGCAAAGAATTTAATCGCTAGACTACATTTCTCAATAGTGGTTATATA
+ATTTCTCTTAATTGAATATAGAGGAATAGTTATGTCTATACTAAATTTATAAAATACAAAAATAGTATTGACAGGAAGTA
+GAAATATTTAGTATAATGAATAAGTTGTCTCGAGAGAGCAGTTTCTATTAGCGCGTAGTTAACAACTTAAAAAAAGTAGT
+TGACAAAGCAGAATAAGTTTGCTAGAATATAGAAGTTGTCTCAAGAGAGGCAAAGACCTTTGAAAACTGAACAAGACGAA
+CGAATGTGCAGGGTGGATTTACATTGTAAATCCGTCAATGACAAAAAACAATAAATCTGTCAGCGAGACAGAAAAGAGCA
+AAGCTCAAACTTTTAATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTAGAACGC
+TGAGGTTTGGTGTTTACACTAGACTGATGAGTTGCGAACGGGTGAGTAACGCGTAGGTAACCTGCCTCATAGCGGGGGAT
+AACTATTGGAAACGATAGCTAATACCGCATAAGAGTAATTAACACATGTTAGTTATTTAAAAGGAGCAATTGCTTCACTG
+TGAGATGGACCTGCGTTGTATTAGCTAGTTGGTGAGGTAAAGGCTCACCAAGGCGACGATACATAGCCGACCTGAGAGGG
+TGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGGAA
+GTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGAGAAGAACGTTGGTAGGA
+GTGGAAAATCTACCAAGTGACGGTAACTAACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
+CCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAA
+CCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAG
+ATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAAC
+AGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAGGTGTTAGGCCCTTTCCGGGGCTTAGTGCCGCAGC
+TAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGG
+TGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTTCTGACCGGCCTAGAGATAGGC
+TTTCTCTTCGGAGCAGAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAA
+CGAGCGCAACCCCTATTGTTAGTTGCCATCATTAAGTTGGGCACTCTAGCGAGACTGCCGGTAATAAACCGGAGGAAGGT
+GGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGTTGGTACAACGAGTCGCAAGC
+CGGTGACGGCAAGCTAATCTCTTAAAGCCAATCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGTCGGAATCG
+CTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTG
+TAACACCCGAAGTCGGTGAGGTAACCTTTTAGGAGCCAGCCGCCTAAGGTGGGATAGATGATTGGGGTGAAGTCGTAACA
+AGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGATAAGGAAACCTGCCATTTGCGTCTTGTTTAGTT
+TTGAGAGGTCTTGTGGGGCCTTAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTA
+GGCTCCATTGAATCGAAAGGTTCAAATTGTTCATTGAAAATTGAATATCTATATCAAATTCCACGATCTAGAAATAGATT
+GTAGAAAGTAACAAGAAAATAAACCGAAAACGCTGTGAATATTTAATGAGTTTTCTAGTTTTAAAGAAACTAGGTTAATA
+AGGTTAAGTTAATAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGAAGAAGGACGTGACTAACGACGAAATGCTTT
+GGGGAGCTGTAAGTAAGCGCTGATCCAGAGATGTCCGAATGGGGGAACCCACTAGTTAATGACTAGTATCCATATCTGTT
+AAGGATATGAGAAGGAAGACGCAGTGAACTGAAACATCTAAGTAGCTGCAGGAAGAGAAAGCAAAAGCGATTGCCTTAGT
+AGCGGCGAGCGAAACGGCAGGAGGGCAAACCGAAGTGTTTACACTTCGGGGTTGTAGGACTGCGATATAGGATTAATCAT
+TATAGAAGAATTACCTGGGAAGGTAAGCCAAAGAGAGTAACAGCCTCGTATTTAAAATGATAGATTAACCTTAGCAGTAT
+CCTGAGTACGGCGAGACACGCGAAATCTCGTCGGAATCTGGGAGGACCATCTCCCAACCCTAAATACTCTCTAGTGACCG
+ATAGTGAACCAGTACCGTGAGGGAAAGGTGAAAAGCACCCCGGGAGGGGAGTGAAATAGAACCTGAAACCGTGTGCCTAC
+AACAAGTTCGAGCCCGTTAATGGGTGAGAGCGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATATGATGCGAGGTTAA
+GTTGAAGAGACGGAGCCGTAGGGAAACCGAGTCTTAATAGGGCGTCATAGTATCATGTTGTAGACCCGAAACCATGTGAC
+CTACCCATGAGCAGGTTGAAGGTGAGGTAAAACTCACTGGAGGACCGAACCAGGGCACGTTGAAAAGTGCTTGGATGACT
+TGTGGGTAGCGGAGAAATTCCAAACGAACTTGGAGATAGCTGGTTCTCTCCGAAATAGCTTTAGGGCTAGCGTCGATGTT
+AAGTCTCTTGGAGGTAGAGCACTGTTTGGGTGAGGGGTCCATCCCGGATTACCAATCTCAGATAAACTCCGAATGCCAAC
+GAGATATAATCGGCAGTCAGACTGCGAGTGCTAAGATCCGTAGTCGAAAGGGAAACAGCCCAGACCACCAGCTAAGGTCC
+CAAAATATATGTTAAGTGGAAAAGGATGTGGGGTTGCACAGACAACTAGGATGTTAGCTTAGAAGCAGCTATTCATTCAA
+AGAGTGCGTAATAGCTCACTAGTCGAGTGACCCTGCGCCGAAAATGTACCGGGGCTAAAACATATTACCGAAGCTGTGGA
+TGACACAAAAGTGTCATGGTAGGAGAGCGTTCTATGTGTGAAGAAGGTGTACCGTGAGGAGCGCTGGAACGCATAGAAGT
+GAGAATGCCGGTATGAGTAGCGCAAGACAGGTGAGAATCCTGTCCACCGTAAGACTAAGGTTTCCAGGGGAAGGCTCGTC
+CGCCCTGGGTTAGTCGGGACCTAAGGAGAGACCGAAAGGTGTATCCGATGGACAACAGGTTGATATTCCTGTACTAGAGT
+ATATAGTGATGGAGGGACGCAGTAGGCTAACTAAACCAGACGATTGGAAGTGTCTGGTCAAACAGTGAGGTGTGATATGA
+GTCAAATGCTTATATCTTTAACATTGAGCTGTGACGAGGAGCGAAGTTTAGTAGCGAAGTTAGTGATGTCACACTGCCAA
+GAAAAGCTTCTAGCGATACATATACTCTACCCGTACCGCAAACCGACACAGGTAGTCGAGGCGAGTAGCCTCAGGTGAGC
+GAGAGAACTCTCGTTAAGGAACTCGGCAAAATGGCCCCGTAACTTCGGGAGAAGGGGCGCTGATTTTAGATCAGCCGCAG
+TGAATAGGCCCAAGCAACTGTTTATCAAAAACACAGCTCTCTGCTAAATCGTAAGATGATGTATAGGGGGTGACGCCTGC
+CCGGTGCTGGAAGGTTAAGAGGAGTGCTTAGCGTAAGCGAAGGTATGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTA
+TAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAATGATTTGGGCACTGTCTC
+AACGAGAGACTCGGTGAAATTTTAGTACCTGTGAAGATGCAGGTTACCCGCGACAGGACGGAAAGACCCCATGGAGCTTT
+ACTGCAGTTTGATATTGAGTATCTGTACCACATGTACAGGATAGGTAGGAGCCTATGATAACGGGACGCCAGTTTCGTTT
+GAGGCGTTGTTGGGATACTACCCTTGTGTTATGGCTACTCTAACCCAGATAGGCAATCCCTATCGGAGACAGTGTCTGAC
+GGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGACTGGTTGGAAATCAGT
+CGTAGAGTGTAAAGGTATAAGGGAGCTTGACTGCGAGAGCTACAACTCGAGCAGGGACGAAAGTCGGGCTTAGTGATCCG
+GTGGTTCCGTATGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCTGGGGATAACAGGCTTATCTCCCCCAAGAGTTCA
+CATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTC
+GCCCATTAAAGCGGCACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGTAGGAAATT
+TGAGAGGATCTGCTCCTAGTACGAGAGGACCAGAGTGGACTTACCGCTGGTGTACCAGTTGTCTTGCCAAAGGCATCGCT
+GGGTAGCTATGTAGGGAAGGGATAAGCGCTGAAAGCATCTAAGTGCGAAGCCCACCTCAAGATGAGATTTCCCATGATTT
+TATATCAGTAAGAGCCCTGAGAGATGATCAGGTAGATAGGTTAGGAGTGTAATTGTGGTGACACATTTAGCGGACTAATA
+CTAATAGCTCGAGGACTTATCCAAAAAGAGATATTGACAACGTTACGGTTTCTTGTTAGACTATAGATATTCAATTTTGA
+GTGAATAAGGCTCAATAGTTAAGTGATAATTGCCTAGGAGATACACCTGTTCTCATGCCGAACACAGAAGTTAAGCCCTA
+GAACGCCGGAAGTAGTTGGGGGTTGCCCCCTGTGAGATAAGGTAGTCGCTTAGCAAAGGGAGTTTAGCTCAGCTGGGAGA
+GCATCTGCCTTACAAGCAGAGGGTCAGCGGTTCGATCCCGTTAACTCCCATAGGTCCCGTAGTGTAGCGGTTATCACGTC
+GCCCTGTCACGGCGAAGATCGCGGGTTCGATTCCCGTCGGGACCGTAGACTCGTTAGCTCAGTTGGTAGAGCAATTGACT
+TTTAATCAATGGGTCACTGGTTCGAGCCCAGTACGGGTCATTTAGAAATGCGGGTGTGGCGGAATTGGCAGACGCACCAG
+ATTTAGGATCTGGCGCTTAACGGCGTGGGGGTTCAAGTCCCTTCACCCGCATTAGTAGATTGCCGGCTTAGCTCAGTTGG
+TAGAGCATCTGATTTGTAATCAGAGGGTCGCGTGTTCAAGTCATGTAGCCGGCATTAACTTTATAATTTTAGAAGTTATT
+TTGGGCGCGTAGCTCAGGTGGTTAGAGCGCACGCCTGATAAGCGTGAGGTCGGTGGTTCGAGTCCACTCGTGCCCATCAA
+GAATATGGTCCGTTGGTCAAGGGGTTAAGACACCGCCTTTTCACGGCGGTAACACGGGTTCGAATCCCGTACGGACTATT
+TTTTGTTATATGGAGGATTACCCAAGTCCGGCTGAAGGGAACGGTCTTGAAAACCGTCAGGCGTGTAAAAGCGTGCGTGG
+GTTCGAATCCCACATCCTCCTTTAAAGATATCGCGGGATGGAGCAGCTAGGTAGCTCGTCGGGCTCATAACCCGAAGGTC
+GTAGGTTCAAATCCTGCTCCCGCAATAGGCTCGGTAGCTCAGTTGGTAGAGCAATGGATTGAAGCTCCATGTGTCGGCGG
+TTCGATTCCGTCTCGCGCCATTTATACCTTAGGAGAGATAGCGAAGAGGCTAAACGCGGCGGACTGTAAATCCGCTCCTT
+CGGGTTCGGGGGTTCGAATCCCTCTCTCTCCATAGTAAACGGGCATAGTTTAAAGGTAGAACTAAGGTCTCCAAAACCTT
+CAGTGTGGGTTCGATTCCTACTGCCCGTGTTTTTTCTAATATGGCGGGTGTGGTGAAGTGGTTAACACATCAGATTGTGG
+CTCTGACATTCGTGGGTTCGATTCCCATCACTCGCCTTTTCATGGGGTATAGCCAAGCGGTAAGGCAAGGGACTTTGACT
+CCCTCATGCGTTGGTTCGAATCCAGCTACCCCAGTTTTAAGATAGCCGGCGTGGCGGAATTGGCAGACGCGCTGGACTCA
+AAATCCAGTGTCCTCACGGACGTGCCGGTTCGACCCCGGCCGCCGGTATATTTATAAAGACAAGGTTTAGAAGCCTTGTC
+TTTTTTGTATTGTGCTGGTAATTTTGAGAAAAAGTTACTGAAAATTACTTATATTTGTTTTTCATTATTGCAATCGTTAT
+AGAAGGTTTAAAACAAGCAGAAATAATAAGGAAATTTTTCAAGAGTTAGTGGAGACTCAACATTTAAATGAAATTCAAAG
+AGGACTCCTAAATGTCATAGGTTCTGAAGTAATAAAAGTGTTTGTGAATGATAGATAGGTAGTATAAAATAATAAGATTT
+TTCAGTGTATATGTTACGACTAAAAAATTAAACTCGTGAAAATTTGTTATACTAATATTAGTTTTAACATACTGGTAAAT
+AATAATTATTTTTATTAGATACTTGACATGGGAAGTTTATTTTCTAAGAAAAGAGAGCATGTTGAAAAAATATGTAAAAT
+GGTTAATTCCCATATCTATTATTGGGATGTTACTAGCAGGCTGTCAAATGAATAGTGAATCTAAAAGTCAGTCAAACGAA
+GTAAAAAATAGCAAACAGTCAGCAGTAAAGAAAGGTAAAAAAGTAATAAAAAAAGAACAAGTAGCTTATCTCAAAAAGCA
+TGAAAAAGAATTAACTGAATATGTCAAAATCCAGATATTAGTGAAATTAAGTATGATTGGAATAGTGTGCGCATAGTGGA
+AGCTAGTAGTGGAACCCCTCAAGGCGGAGAGCAACTATTATTAATTTTGGGTTATGCAAATGGCAGTGAATTAACCAATT
+TTACTCTAAATTTCACATTGGGTGATAATCAAATGCCTAATATTGACTCAGTTGGCTCAGATAATTTATCAACTATTGAA
+GATTAATAATAACAATAAGAAAGGTATATAATGGGATGATGGAATCTTAAGGAATTTGAAGATATATTTTGAAGTATGGC
+AGAAAGTGCTAATACAGGTCGATCGAATTCTTTTGTTTTAGAAGAATTAACTGAATTTCAAAGAGAAAAGTTAAAAAATG
+GGGAGTCAGTTAAGTTTAATTTTTCTAAAGATGTTAAGAAAGAAAATAAGGTTATCGAAGGAGGGCACCCCCAAGTCATA
+GGGTAATCTACCTGCAAACTGGATAAGTCCTTAAATACAATTGATGAAAAAGTAGAGGTTCGCGTTCCTGATGTCAATGG
+CGGTTATCACTCTGAGCATTGTGTTACTAATTCCTATCAGAAAGGTTACTGAAAGATGATGAAGCAGTAACTCTATAATC
+ACTAAAAGCTCATCATTGCTTAGTGTTTAAGTTAACTTCTAAAGCTCAAACCTTGTTAAATCAAGGTCTGTTTGCTTTTA
+AAAGTGACATGTTATTTTTCTAAAAATGAGATTATTGGGATTCCTCATTCTAAGTTACTTTGTTTATATGTACCTTTACT
+TAAGGTTTATTTTCATTATTTTTAATTTAATATTTTGGAGTATGTATGCTCCATTATAGTATTTTCGAAGACATCTTTAA
+AAGGACTGTAGAAGTTAAAATATTTTAACCTAGTATCTAACGTCATATATTGGTACATAGTTTTAAGTATCCTTTTGATA
+ACCTTGTACATATGAAATAGGCTAGATATTTTTAGTGAACTAAATGTAAGTTTATTGCTTGTATTAGGCGGGATAACAAT
+ATTGTTGTTTTTATTCTTTCTGAGTAATGGTTTATTAATCATGTAATTATTCTGGTATCAAATGATACTTTTAATATTCC
+AGTTTGTCAATAAATCATCAATGTAATTCTTTTCATCAAAAGCGATCCCTTTATCTAGTTGATTTAATATGTTAACTTGA
+TGATTGTTCTTCTTGCTTAATATATGGGATAATAATTATCTTAAATTGACACTTGGAGCATTCAATCACGTGATGTAATA
+ACTAAAAATTGTTTAAAATTTAAGGATGTATTTCTTGTTGATCTTACTATCTGATCTAATAATAGTATATAATAAGATTA
+AAATTTAAACATTGTCTGGAGATGTAGCAAAGGAGATAAAATGACTAAAATTTATCATATGATTTTATGTAATTCTGATA
+TAATGAAGATTTTAGCTATAATAAAATCTCTTCCACTGAATGATTGTTGGCTGTGTGCTGGCACATTGAGAAACTTTGTA
+TGGAATAAACTTTCTGGAATAAATGAGACATTGACATCAGATATTGATGTTGTATTTTTTGATAAAAATATTTCTTATGA
+AGAAACGGTGGTATTAGAACAACAATTAAAGGATAACTATCCACAGTACGATTGGGAACTTAAAAATGAATTTTACATGA
+ACACTCATTCTCCTAATACCCCAAAGTATACTAGCTCTAAAGATGCTATTTCAAAATTTCCTGAAAAGTGTACTGCAGTG
+GGAGCAAGGTTAGATGATAGAAATCAACTCGAACTTTACCTCCCTTATGGTGAAGAGGAAATATTAAATTTCATTGTTAG
+TCCTACGCCATATTTTGAAGAGGATCTATTACGTTATAATGTTTATTTGAAGCGAGTGGATAAGAAGAAATGGAATAATA
+TTTGGCCTCGTTTAACAATCATAAAAAAATGATAACGTTACTGGAGTTGGCTTAACAGCTTTTAAATTTTTAGACTGACA
+AATAGTATAGACCTTTAATAAGGTCGTTTATCGATAATCATAGTGTACTGTGTTATAATCGTTATAGCATAAAAACACGT
+TGCAGTTGGTAGTCTGCAAGCGTTCAGTGAACGTCAGTAACCTTCCCTCCAGGTCGTCCATTGCAATTTAATATTTAAAG
+GAGGGGGCTGTATGAAAATGACAGTCTATTTTGATGGTAATTTTTGGTTGGGTTTGATTGAGTACGATGATGATGGTGAT
+TACAAAGTTTTTCGGTATTTTTTTGGAAAAGAACCTAAAGATGATGATGTTTTTAATTTTATAAATCATAAACTTAATGA
+TTTGATAAAAAAATATGAGTTTGTTAAAACGGATATTTCTCTAAAGCGTACGAATGAACACAAAAAAAGTCCTAAAAGAA
+TGCAAAGAGAAATTAATAGAGAAAAACGTAAGCCAGTAGTATCTACAAAAGCGCAATTGGCGATGAAAACTATTCATATG
+AGTATAAAAAACGAACGTCAATTAAGTCAGAAATGTAAGAAAAATGAGTTAAGAAAACATCGGTACCAATTAAAACAAGA
+AAAACGTTACCAAAAGAAAAAAGGACATTGATTGTGTCATCATATAAAAAGCTTGAGAGTGTCATCTCAAGCTTTTTATA
+TGTTAACTAATATGAGTCACTAAATAGTCTGATAATGCTCAATTAATGTGTTTTGGGAAAAAATCATTTCCTTAAAGGAC
+ACCATTGTCATGTTGTTATCACCTTACTTTTTTTATACTTAGTATATGTTTAAGAAAGGAATAAGTTGTTTTGAGAGATT
+TTGAGGAGTTGTTTGATAAAGTAAAGCCAATCGTAATGAAGCTGAGAAGAAATTATTTTGTTCAACTTTGGGAATATGAT
+GATTGGATTCAAGAAGGACGTATTGTACTTTTTAGGTTGCTTGAAGAGCATCCGTATTTATTGGATAATGAAAGCAAACT
+ATTCATTTACTTTAAAACAAAATTTTCAAATTATTTAAACGATGTATTAAGACACCAAGATTGTCAAAAGCGACAATTTA
+ATAAAATGCCTTATGAAGAAATAAGTGAAGTTAGTCACTATGTTAAGAGTAAAGGACTAGTTTTAGATGACTATATTGCT
+TATCGTGATACTTTAACAAAAGTGGAAGAAACTTTGTCAGATATTGATAAAGAAAAATTTGAAAAACTGATTAGTGGTGA
+ACGTTTTGCGGGGAAGAAACAATTCATACGAGATATTCAACCCTTTTTCAATGCTTTTAAAGCGGATTAATCGATTTTAT
+TTCTGCAGTAGATAGCTGCAGAATTTTTTTATAGGGAAAGTTCGCTGATATATTCCTGTGAAAGCCTTTGTTTTTTGTTA
+TAATATAATAAAATGCTTGTGAGGTGTCAGTATGAGTAAAGTTCGTTTATATATCGCTCGTCATGGTAAAACAATGTTTA
+ATACAATTGGTCGCGCTCAGGGGTGGAGTGATACTCCTTTAACTACTTTTGGAGAACTCGGGATTAAAGAGCTTGGTTTG
+GGACTAAAGGCTTCAAATATTAGTTTTAAAGAGGCTTTTTCTAGTGATAGTGGACGTACTTTACAAACTATGGAAATTAT
+TCTCAGGGAAGTGCAACAAGAAAATATTCCCTATACGAGAGATAAACGAATCCGCGAGTGGTGCTTTGGTAGTTTGGATG
+GAGGATATGATGGCGACCTTTTTAATGGCGTTCTGCCTCGAGTTTCAAACGGAGATATGAGCCATTTGACACACGAAGAA
+ATTGCTAATTTGATTTGTCAAGTTGATACGGCTGGCTGGGCAGAACCGTGGGCAATATTGAGTAACCGTATTCTGTCAGG
+CTTCACTGCTATAGCTAAAAAAATAGAGGATATTGGGGGAGGTAATGCGATTGTTGTCAGTCATGGGATGACTATTGCGA
+CTTTTTTATGGTTAATCGACCATAGTACCCCTCGTAGTTTAGGCTTAGATAATGGTAGTGTCTCAGTCGTTGATTTTGAA
+GATGGAACATTTTCTATTCAATCTATTGGGGATATGTCCTATCGAGAAAAAGGAAGAGAAATTTTAGAAAAAACATTGCA
+ATGAAAAAAAATAAAATTATCCGATTCAGTTTAGTTGGTGTTCTACTTGCGATACTATGCTTTAGTCTTTTTGCTTTATT
+GAAGCCTAACAGTCAACAATCATCATCTCAAAAGTTGAGGAATGAGGATATAAAAAAGATATCCTCTCAAAAAAGAAATA
+AGAAATTACAATTACCAGCTGTATCATCAAAAGATTGGAACTTGATTTTGGTCAATCGTGACCATAAACATGAAGAATTA
+AGTCCAGATGTGGTTCCTGTTGAAAATATTTATTTGGATAAACGTATTACGAAGCAAGCTACTCAGTTTTTAGAGGCTGC
+TAGAGCAATTGATTCACGAGAACATTTAATTTCGGGTTATCGTAGTGTTGCCTATCAGGAGAAGTTGTTCAATTCTTATG
+TTACTCAAGAGATGACTAGTAACCCTAATTTGACGAGGGGACAAGCAGAAAAGTTGGTAAAAACTTACTCTCAGCCTGCA
+GGTGCTAGTGAACACCAGACTGGATTAGCGATGGATATGAGTACTGTAGATTCTTTGAATGAGAGCGATCCTAGAGTAGT
+CAGTCAGTTGAAAAAGATAGCTCCACAATATGGTTTTGTCTTACGGTTTCCGGATGGTAAAACAGCAGAAACAGGGGTAG
+GTTATGAAGATTGGCATTACCGCTATGTTGGGGTAGAGTCTGCAAAATATATGGCCAAACATCATTTAACATTAGAAGAA
+TACATAACTTTATTAAAGGAGAATAACCAATGAGGAAACGTTTTTCCTTGCTAAATTTTATTGTTGTTACTTTTATTTTC
+TTTTTCTTTATTCTTTTTCCGCTTTTAAACCATAAGGGAAAAGTAGATGCTAATTCTAGGCAGAGTGTTACCTACACCAA
+AGAAGAATTTATACAAAAAATTGTGCCAGATGCGCAAGATCTAGGAAAGTCGTACGGTATTCGTCCTTCATTTATTATTG
+CACAGGCGGCTTTGGATTCTGATTTCGGAGAGAAAATATTAGCTAATAAGTATCATAATCTGTTTGGTTTGCTTGCAGAA
+CCAGGAACGCCCTCAATTACCTTAAATGATAGTAGTACAGGAAAAAAACAGGAAAAGCAATTTACTCATTATAAATCTTG
+GAAGTATTCAATGTATGATTACCTTGCTCATATAAAATCTGGAGCGACAGGCAAAAAAGATTCATATACTATAATGGTGT
+CTGTTAAAAATCCAAAAACTTTAGTGCAAAAATTACAAGATAGTGGTTTTGATAATGACAAAAAGTACGCTAAAAAAATG
+ACGGAAATCATTGATTTGTATGATTTAACAAGATATGATAAGTGATATTAGCACTCTTTGAATAAGAGTGCTAATTTTTG
+ATGTTTTTTCCTTGACTATCTTTTAAAAAGGAGTATAATAAAATCATAGTTAGCAGTCGATGTGTAAGAGTGCTAATTTC
+AGAAAGACCGAGAGGGGTGATGTTTTTGTGATTACACAACGTCAAAATGATATTTTGAATTTAATCGTTGAGTTATTTAC
+ACAAACTCATGAACCAGTAGGGTCTAAAGCTTTACAGAGAACGATTGATTCTAGTAGCGCCACTATTCGTAATGATATGG
+CAAAACTAGAGAAGTTGGGGTTATTGGAAAAAGCACACACTTCTAGTGGACGGATGCCGAGTCCAGCTGGTTTTAAGTAT
+TTTGTAGAGCACTCCCTTAGACTAGATAGTATTGATGAGCAAGATATTTATCATGTTATAAAAGCTTTTGACTTTGAAGC
+ATTCAAATTAGAAGACATGCTTCAAAAAGCTAGTCATATTTTATCGGAGATGACGGGCTATACATCCGTTATTTTAGATG
+TGGAGCCAGCTCGTCAACGTTTGACAGGGTTTGATGTTGTTCAGCTTAGCAACCATGATGCTCTAGCAGTCATGACTTTA
+GATGAATCTAAGCCAGTGACAGTGCAGTTTGCTATTCCAAGAAACTTTTTGACACGTGACTTGATAGCATTTAAAGCTAT
+CGTAGAGGAGCGCTTGCTGGATGGTAGTGTCATGGATATTCATTATAAGTTGAGGACAGAAATTCCTCAGATCGTTCAGA
+AGTATTTTGTAACTACGGATAATGTTTTACAACTATTTGATTATGTTTTTTCAGAGCTGTTTCTGGAAACGGTATTTGTA
+GCTGGCAAGGTAAATTCTTTAACGTATTCAGATCTATCAACGTATCAGTTTTTGGATAATGAGCAGCAAGTAGCGATTTC
+TTTGAGGCAAAGTCTGAAAGAGGGTGAGATGGCTTCTGTCCAAGTGGCAGATAGTCAAGAAGCCGCACTTGCAGATGTGT
+CAGTTTTAACTCACAAATTTTTGATTCCTTACCGTGGATTTGGACTCCTGAGTTTGATTGGTCCTATTGATATGGATTAT
+CGTAGGTCTGTTAGTTTGGTAAACATTATCGGAAAGGTATTGGCTGCTAAATTAGGTGATTATTATCGATACCTAAATTC
+TAACCATTATGAAGTTCACTGATAATGGCAGTATTCAATAAGTTATTTAAAAGGAGGCACTCAGTGTCAGAAGAAATTAA
+AAAAGACGATTTACAGGAAGAAGTGGAAGCCACTGAAACTGAAGAGACAGTTGAGGAAGTTATTGAAGAAATTCCTGAAA
+AATCAGAGTTAGAACTCGCAAACGAGCGTGCTGATGAGTTTGAAAATAAATACTTGCGAGCTCATGCAGAAATGCAGAAT
+ATACAACGTCGCTCTAGTGAAGAACGTCAACAACTTCAACGCTATCGTTCTCAGGATCTGGCAAAAGCAATCTTACCATC
+GCTTGACAATCTAGAACGTGCCTTGGCTGTTGAAGGGTTGACAGATGATGTTAAAAAAGGTTTAGAAATGACTCGTGATA
+GCCTTATTCAAGCACTAAAGGAAGAAGGCGTAGAAGAAGTAGAAGTCGACTCATTTGACCACAACTTTCATATGGCAGTT
+CAGACTCTCCCAGCCGATGATGAACATCCAGCCGATAGCATTGCAGAAGTCTTTCAAAAGGGATATAAATTGCACGAGCG
+TCTGCTAAGACCAGCGATGGTAGTTGTCTATAACTAAGGTAAATGAGTTTTCGTTTTTGTCCGTAATGACAGTAAACTAG
+ATAGCAAGTTAGAAGCTATTCAGCTTGCTGATTAAACTATAGTGATTGCTTAGAATTGGAAGTAAAATAATTCGAGTGCT
+TACTAAGATAAATTGAAATAAAAAGTAATAAAGTATTATAAAATAAGAGGTATTAACATGTCTAAAATTATTGGTATTGA
+CTTAGGTACAACAAACTCAGCAGTAGCAGTTCTTGAAGGGACTGAATCAAAAATCATTGCTAACCCAGAAGGCAATCGTA
+CAACTCCTTCAGTAGTATCATTCAAAAATGGTGAAATTATCGTGGGTGATGCTGCAAAACGTCAAGCGGTAACAAATCCA
+GATACTGTTATCTCTATCAAATCAAAGATGGGAACTTCTGAAAAAGTTTCTGCAAATGGTAAAGAATATACTCCTCAAGA
+AATTTCAGCAATGATTCTTCAATACCTTAAAGGTTATGCTGAAGACTATCTTGGAGAAAAAGTAGAAAAAGCAGTTATTA
+CTGTTCCAGCTTACTTCAACGATGCACAACGTCAGGCAACTAAAGACGCTGGTAAAATTGCAGGTCTTGAAGTAGAACGT
+ATCGTTAACGAACCAACAGCAGCCGCACTTGCTTATGGTATGGACAAGACTGACAAGGATGAAAAAATCTTAGTTTTTGA
+CCTTGGTGGTGGTACATTTGACGTATCAATCCTTGAATTAGGTGATGGTGTCTTCGACGTTCTTGCAACAGCAGGTGATA
+ACAAACTTGGTGGTGACGACTTTGACCAGAAAATTATTGATTTCTTGGTAGAAGAATTCAAGAAAGAAAATGGTATTGAT
+CTTTCTCAAGACAAAATGGCTCTTCAACGCTTGAAAGATGCTGCTGAAAAAGCTAAAAAAGACCTTTCAGGTGTAACTCA
+AACTCAAATTTCATTACCGTTCATCACTGCTGGTTCTGCTGGTCCTCTTCACTTGGAGATGAGCTTATCACGTGCTAAAT
+TTGACGATCTCACTCGTGACCTTGTTGAACGTACGAAAACTCCAGTTCGTCAAGCTCTTTCAGATGCAGGCTTGTCATTG
+TCAGAAATTGATGAAGTTATCCTCGTTGGTGGATCAACACGTATCCCAGCAGTTGTTGAAGCTGTAAAAGCTGAAACTGG
+TAAAGAACCAAATAAATCTGTTAACCCTGATGAAGTGGTTGCTATGGGTGCTGCTATCCAAGGTGGTGTTATCACTGGGG
+ATGTGAAAGACGTTGTACTTCTTGACGTAACACCATTGTCACTTGGTATCGAAACAATGGGTGGTGTCTTCACTAAATTG
+ATCGACCGCAACACAACAATCCCAACATCTAAATCACAAGTCTTCTCAACAGCAGCAGACAACCAACCAGCCGTTGATAT
+CCATGTTCTTCAAGGTGAACGCCCAATGGCAGCAGATAACAAAACACTCGGTCGCTTCCAATTGACTGATATCCCAGCTG
+CACCTCGTGGAATCCCACAAATTGAAGTAACATTTGATATCGATAAAAATGGTATTGTATCTGTTAAAGCTAAAGATCTC
+GGTACTCAAAAAGAACAACACATTGTTATCCAATCTAATTCAGGATTAACTGATGAAGAAATTGATAAAATGATGAAAGA
+TGCTGAAGCAAATGCTGAAGCAGATGCAAAACGTAAAGAAGAAGTTGATCTTAAAAATGAAGTTGACCAAGCCATCTTTG
+CAACAGAAAAAACTATTAAAGAAACTGAAGGCAAAGGCTTTGATACAGAACGTGATGCAGCGCAATCAGCACTTGATGAG
+TTGAAAAAAGCTCAAGAATCAGGTAACCTTGACGACATGAAAGCTAAACTTGAAGCTCTTAACGAAAAAGCACAAGCTCT
+TGCAGTTAAACTTTACGAACAAGCGGCTGCAGCACAACAAGCAGCTCAAGGGGCTGAAGGTGCACAATCAGCTGATTCAT
+CAAGCAAGGGTGATGATGTTGTAGATGGCGAATTCACTGAGAAATAATTATTAATATTGTTCAGATTCATTTGAATATAA
+GCATGAAAACTATACTAGCATAGTAAAGTTCTTCGTGATAGGGGTTGCTCAATAATCTAGATAAGTTTCAGATTACATAA
+GCTAATTTCGCTATCACTAAATAAAAACATATTAATAATAAATAGGCGGGGCGCCTCGCTCCGTCTGTTTTATTAAGTGT
+CATATATATGTTAACTATTTAGAGCTGTAACTGGGCAAGAATAATTGTTAATCTCTTCAAGTGTAGTATATGAACAAAAT
+ATAAAGGATTAGATAATGAACAATACAGAATTTTATGATCGTCTTGGCGTTTCAAAAGATGCTTCTCAGGACGAAATAAA
+AAAAGCTTACCGTAGGATGTCTAAGAAATACCATCCAGATATTAATAAGGAGACGGGAGCAGAGGAAAAATATAAAGAGG
+TTCAAGAAGCTTATGAAACCTTGAGTGATACACAAAAACGTGCTGCCTATGATCAATATGGCGCTGCTGGGGCAAATGGC
+GGTTTTGGTGGCTTCGATGGTGGCGGTTTTGGTGGCTTCGATGGTGGTGGCTTTGGTGGTTTTGAAGACATCTTCTCAAG
+CTTTTTTGGTGGAGGAGGGATGCGCAATCCTAATGCACCACGTCAAGGAGATGACCTACAATATCGTGTTAATTTAAGTT
+TTGAAGAAGCTATCTTTGGAGCTGAAAAAGAAGTATCTTATAATCGGGAGTCATCATGTCATACTTGTTCAGGAAGTGGA
+GCTAAGCCAGGTACTAGCCCTGTGACTTGTCAAAAGTGTCATGGTTCGGGTGTGATTAATGTTGATACACAAACACCTCT
+AGGAACAATGCGTCGCCAAGTGACTTGTGATGTTTGTCAGGGTAGTGGTCAAGAAATCAAAGAGAAATGTCCAACATGTC
+ATGGAACTGGTCATGAGAAGAAGACGCATAAAGTATCAGTTAAAATACCTGCAGGAGTTGAAACTGGGCAACAAATTCGT
+TTAACAGGACAAGGTGAAGCTGGCTTCAATGGTGGTCCTTATGGTGATCTCTTTGTTATTATTAACGTTCTCCCAAGCCA
+ACAGTTTGAGCGTAATGGATCAACAATTTATTATACTTTGAATATTAGCTTTGTCCAAGCTGCTTTGGGTGATACAATTG
+ATATACCTACTGTCCATGGAGCGGTAGAAATGTCAATTCCTGCTGGTACTCAGACAGGAAAAACGTTTCGTCTTCGCGGA
+AAAGGTGCCCCTAAACTTCGAGGGGGTGGACAAGGTGATCAGCATGTTACTGTTAACATCGTAACTCCTACTAAATTGAA
+TGATGCTCAAAAAGAGGCATTGCACGCTTTTGCAGAGGCAAGTGGAGATAAGATGGTACATCCGAAGAAGAAAGGTTTCT
+TTGATAAAGTCAAAGATGCTTTAGATGTTGATTAAAAAATAAAAGTCTAGAATCGAAAGTATTCTAGACTTTTTTGTATT
+GCTAGAGGGATTGCTTGAACCTAAATTTTACAGTACAATGAATCTAATATTGTAGGGGGACAATTTTTATGGTAACCAAA
+GTTGAAGAGATTCGCTCATATTTGATAGCTTCTATACAAAATGGTAAGTTGGCTCCAGGAGATCGCCTACCATCTATAAG
+ACAGTTAGCTAATCAATTTTCCTGTAACAAAGATACAGTCCAACGAGTTTTGATGGAATTGCGTTTTGATAATTATATCT
+ATGCAAAGCCTAGGTCAGGCTATTACGTCTTTGATTCTCATCAAGAGGAAGTTGAAGAAGGGGTTAGTTTACCAAACTCT
+GAGATTGCAAATATAGCTTATGATGATTTTAGATTGTGTTTGAATGAGACCCTTATTGGTAGGGAAGATTACCTTTTCAA
+TTATTACTATCGTCAAGAAGGTCTTCTTGATTTAAGTAAAGCAGTGGCTAAATTAATGGAAGAAACAGGGGTCTATGTTC
+CCCTTGATGATATTGTTATTACGGCTGGTACTCAACAGGCATTATTTATTTTGACACAGGTTACCTTTCCAAATCGAAAA
+TCTCGAGTTTTAATAGAAGAACCGACCTATCCTCGTATGATTGAACTAATCAAAACACAAAATTTACCCTATGAAACTAT
+TTCTCGAGGTACTCATGGAATTGATTTTCAGCGTTTAGAGGAGATTTTCCAGACACAATCAATTAAGTTTTTTTATGTTA
+TACCTCGCATGCATAATCCTTTGGGAACATCCTATAATCCGGTAGAGATGAAAAGATTAATAGAGATGGCAGAGAAGTAT
+GATGTTTATATTGTGGAAGATGACTATATGTCTGATTTTGCAAGTCAGTCACCATTACATTATTATGATACTCACGGGCG
+TGTTATTTATCTAAAATCTTTTTCAAAGGCTATTTTCCCTGCTTTAAGATTAGCTGCGATTTGTTTACCACAAGCTTTAA
+AATCAACATTTATGGCTTACAAGAAGTTGATGGATTATGATACTAATCTGATTTTACAAAAAGCATTAGCGCTTTATATT
+GAAAATGGCCTTTATGCTAAGAATAGTCAATATTTGAAATATCGTTATCAGAAAGACCTTGCAAATTCAAAATCTATTTT
+AGCTGATCACCCTAATCTACCCTCATATAGTTTACATCACGATAGTGTATTATTTGATTGTTCGAAACTCGATAACTTTA
+AAATATTACGGCAATACGGCGATACTTTGGAAAATTATTTTTGTCAAAAATCGCATCAATCTCTCTTACAAGTAAAAAAT
+GATTCCTGCTTAAAGCAGTTCTTGGGATCGTTGTAGTATAATTGTAGGGGGACAGTTTAAAATAGATAATATAGTTTTCA
+TAAATGAAAGGTGGTAAAATAAACCCATGACAAGGTATAAGGCACAGATTTCTTATGATGGTTCAGCTTTTTCAGGCTTC
+CAAAGACAACCAAATTGTAGGACAGTTCAAGAAGAAATTGAGAGAACTCTTAAGCGCCTAAATAGCGGGAACGATGTGAT
+AATCCATGGTGCTGGTCGCACAGATGTTGGTGTTCATGCTTATGGACAAGTTATCCATTTTGATTTACCACAGGCGCGTG
+ATGTAGAAAAATTACGCTTTGGTTTAGATACACAGTGTCCAGACGATATTGATATTGTCAAAGTAGAGCAAGTGTCTGAT
+GATTTTCATTGTCGATATGATAAACACATTAAAACTTATGAGTTTTTAGTGGATATCGGTAGGCCGAAAAATCCTATGAT
+GAGAAACTATGCAACACATTACCCTTATCCTGTCATTATTGAGCTTATGCAAGAAGCTATTAAAGATTTAGTAGGTACCC
+ATGACTTTACAGGCTTTACTGCTTCAGGTACGAGTGTAGAAAATAAAGTACGTACTATTTTTGATGCGAAAATTCAGTTT
+GAAGCGTCTAAAAATCTTTTAATTTTTACCTTTACAGGAAATGGTTTTTTGTATAAACAGGTGCGTAATATGGTTGGTAC
+CCTGCTAAAAATTGGTAATGGACGCATGCCTATTAGCCAAATCAAAACAATTTTACAGGCTAAAAATCGGGATTTAGCAG
+GTCCAACTGCGGCAGGAAATGGTTTATATTTGAAGGAGATTATTTATGAAGACGAGGAATGTTTTAGCAATTTCAGGAAA
+TGATATTTTCTCTGGCGGCGGCTTGCATGCAGATTTAGCAACTTACGTTGTTAATAAATTACATGGTTTTGTGGCAGTAA
+CATGCTTAACAGCAATGTCAGATAAAGGGTTTGAAGTCATTCCTATAGAGGCATCTATACTAAAGCAGCAACTAGAAAGT
+TTAAAAGATGTAGAGTTTGGGTCTATTAAACTAGGATTGCTTCCCAATGTAGAAACAGCACAAGTTGTTTTGGAATTTGT
+AAAATCAAAACAAGAATGTCCAGTAGTCTTAGACCCAGTCTTAGTTTGTAAAGAAAATCATGATTTAGAAGTTAGCCAAT
+TACGTGAGCAGCTAATTGCGTTTTTCCCATATGCTGATGTGATTACTCCTAATTTAGTAGAGGCTCAATTATTGACGGGT
+CTTTCGATTGAAAACTTAGATCAAATGAAAATTGCTGCTGAGAAACTTTACGATATGGGAGCTAAACATGTTGTTATCAA
+AGGGGGCAACCGTTTAAATGCTGAAGAGGCTACAGACCTTTACTATGATGGTGAACGTTTTGAAACCTATGTTTTTCCTG
+TAGTAGATGCCAATAATACAGGTGCTGGATGTACATTTGCGTCAAGTATTGCCAGCCAATTAGCTATGGGTAAAAATGTA
+GAAGATGCAGTCAAAATGTCTAAAGGTTTCGTCTATCAAGCTATTAAAGCATCGGATAAGTACGGAGTTGTCCAACATTT
+TTAGGAGATTTTAATGAGGAAAGAGAAAACTAGTCAATTGGTTCAATTGGCAATTGTAACAGCTATATCTATTGTATTGG
+GGATGTTTATAAGTATTCCGACACCAACAGGTTTTTTGACATTACTAGATGCTGGAATATTCTTTGCTGCCTTTTACTTT
+GGCAAAAAAGAAGGGGCTGTGGTAGGTGCCTTAGCTGGTTTTTTAATTGATTTATTGAAAGGTTATCCCAATTGGATGTT
+CTTTAGTTTATTGATTCATGGGACGCAAGGGTATTTAGCGGGTTTACCAGGTAGAAGACGTCTTTTAGGTCTTATTAGTG
+CAACTCTTGTTATGGTATTAGGTTATGCTATAGCTAGTGGATTGATGTATGGTTGGGGAGCTGTTCTACCAGATATTCCT
+GGCAATATTATGCAAAATATGGTTGGTATGGTTGTTGGTTTTGCTCTTAATAAGTCTCTAGAAAGAGTGAAGAAATGATA
+CTAGATTATAATAAGTTAAAGCAGGAAACTAAAGCTATTGTAGTTGATATTATTGAACGTAGCGCTCTTAAAAAAGGTCA
+AATTTTTGTACTAGGTCTATCATCTAGTGAGGTTTCTGGTGGTTTAATTGGAAAAAATTCTAGTTCTGAAATTGGTGAAA
+TTATCGTTGAAGTTATCCTCAAAGAGTTACATTCACGCGGCATCTATTTAGCAGTTCAAGGTTGTGAACATGTTAATAGG
+GCGTTGGTTGTTGAAGCAGAATTGGCTGAACGTCAACAGTTGGAAGTCGTTAATGTTGTTCCTAATCTACATGCTGGCGG
+TAGTGGTCAGGTTGCAGCTTTTAAGTTGATGACATCACCAGTTGAGGTTGAAGAAATTGTGGCACATGCTGGAATTGATA
+TTGGAGATACTTCTATTGGAATGCATATCAAGAGAGTACAAGTTCCCTTGATTCCAATTAGTCGTGAGTTGGGAGGAGCA
+CACGTTACAGCACTAGCTAGTCGTCCTAAATTAATTGGCGGTGCTAGAGCAGGATATACGAGCGATCCAATCCGTAAATT
+TTAAAATAAACCTCTGCTCTGCAGAGGTTTATTATTTATCTCAACGAGAGTGGTTATTGGAGAAATTGTACGTTGGTAAG
+TCAATACCTTCTTCAAGAATAGCTTTTTGATAAAGTTTGTAAAATTCAGCATAGATGTCAAACTGAGCACCGTTTTGCGT
+GAAGATATTAATACGATAAACAAATTGACCATTAGCATTGGTTGTAGGACCAAAAACAGTAGGCTCTCCAACGATAGCAG
+GGTGTTTTGAAACATACTCTTCATTGATTTTTGTTACAATATCAGAAATCTGATCAAGGTTTGTATGAACAAATAAAGGA
+ATATCAATTTGAGCACGCATATTGCTACGAGACTTATTGCTGACAATTGTAATATTACGATTAGGAATGAAGTGCAAGGT
+TCCATCGAAATCATGAATTTGTGTGGTGCGTATCCCAACATTAGTAACAGTGCCTGATACAGTACCAACATTAATAATAT
+CACCAACATCAAATTGGTTTTCTAGCAGAATAAAAAAGCCATTGACAACATCTGATAAGAAGCCTTGAGCACCAAGTCCA
+ATAGCAACCCCAGCAATACCAGCCCCAGCTAATAAACTAGAAATTGGAACGCCCAATATACTTAAAATCCAATAGAATAG
+AAAGAAATAAAGGGTATAGTTTAAAACATTGTGAGAAAGTTTAGCTAATGTTTTTTGACGAGCTACTTTTTGTCTAGAAA
+AGGCGAGTGAGCGATTAACAGTCTTTTCGAAAAGATAATTGATGACTTGCCTAACGATAACGAATGCAATGATTAATAAT
+AAGATTGATATTAGTTTGGTGAAGAAAGTAAATAAAACTTCCTCTACATTAAGATGGTCTATAAATTTTTCTAAAGTAAT
+CATAGTAATAGTCTAGTAAAAAAAAAGCCATAGAGCAAGTATTTTAAAAGCTTATCGTTAAGCAGTTTAAAGCTTCTTTT
+TTGCATAAAAACTTTGTAAAACGTTTTAAATTATGGTAAACTAAACTGTATCTAAATAATTTTAAGGAGAAATGACTTAA
+TGTCTACATCATTTGAAAATAAAGCTACAAACCGTGGTATTATCACATTTACAATTAGTCAAGATGAGATCAAGCCAGCT
+CTTGATCAAGCATTCAACAAAGTAAAAAAAGATTTGAACGTTCCAGGATTCCGTAAAGGACATATGCCTCGTACAGTTTT
+CAACCAAAAATTTGGTGAAGAAGCACTCTACGAAAATGCATTGAATTTAGTGTTGCCAAAGGCTTACGAAGCAGCTGTTG
+CAGAACTTGGTTTAGACGTTGTTGCTCAACCAAAAATTGATGTTGTATCAATGGAAAAAGGTCAAGATTGGAAGTTGACA
+GCTGAAGTTGTTACAAAACCAGAAGTTAAACTTGGAGATTACAAAGACCTTTCAGTAGAAGTTGATGCTTCAAAAGAAGT
+TTCAGATGAAGAAGTTGATGCTAAAGTTGAACGTGAGCGTAACAACCTTGCAGAATTGACTGTTAAAGATGGTGAAGCAG
+CACAAGGTGATACAGTTGTTATTGACTTTGTAGGTTCAGTTGATGGTGTTGAATTTGATGGTGGTAAAGGAGATAACTTC
+TCACTTGAACTTGGTTCAGGTCAATTTATCCCAGGATTTGAAGAACAATTAGTAGGTTCTAAAGCTGGTCAAACTGTAGA
+CGTTAATGTAACATTCCCAGAAGATTATCAAGCAGAAGATCTTGCTGGTAAAGATGCTAAATTTGTTACAACAATTCACG
+AAGTAAAAACTAAAGAAGTTCCAGCACTTGATGATGAACTTGCAAAAGATATTGATGATGAAGTTGAAACACTTGATGAG
+TTGAAAGCGAAATATCGCAAAGAGCTAGAATCAGCAAAAGAAATTGCATTTGATGATGCAGTTGAAGGTGCAGCAATCGA
+ATTAGCTGTTGCCAATGCAGAAATTGTTGAATTACCAGAAGAAATGGTCCATGATGAAGTACATCGTGCTATGAATGAGT
+TCATGGGTAATATGCAACGTCAAGGAATTTCACCAGAAATGTACTTCCAATTAACAGGTACAACTGAAGAAGACCTTCAT
+AAGCAATACCAAGCAGATGCTGACAAACGCGTTAAAACTAACCTTGTTATCGAAGCAATTGCAGCTGCAGAAGGCTTTGA
+AGCAACAGATGAAGAAATCGAAAAAGAAATCACAGATCTTGCTTCAGAATACAATATGGAAGCTGACCAAGTACGCGGTC
+TACTTTCAGCAGATATGCTTAAACATGATATTGCAATGAAAAAAGCGGTTGACGTTATCACTAGCTCAGCTACTGTAAAA
+TAATTGCTTATTAAATTTTGAAAAGATTGGGCTTCCCAGTCTTTTTATTTGTGATTATTCTTTTGACGAATAGCTAAAAA
+TAGCGTAAAATAGTAAATAGCGAAAATTTGAAAATATGACTTATCTATTTTCTATCTATAAAGAATATTGCTAAACAAAA
+TGATAGTCTTACACAATTAAGGAGAATAACTTTGGAATTAGAAGTATTTGCTGGGCAAGAAAAAAGTGAACTTTCGATGA
+TTGAAGTTGCTCGCGCTATTTTAGAGCAACGTGGTCGTGATAACGAAATGTACTTCAGCGATTTGGTAAATGATATTCAA
+ACCTACCTTGGAAAATCTGACTCAGCAATCCGTGAGTCATTGCCATTTTTCTATTCAGATTTGAATACAGACGGAAGTTT
+TATTCCACTTGGCGAAAACAAATGGGGACTTCGTTCATGGTATGCTATCGATGAAATTGACGAGGAAATCATCACTCTTG
+AAGAAGATGAAGATGGCGCTCCAAAACGTAAGAAGAAACGTGTCAATGCTTTCATGGATGGTGATGAAGATGCTATTGAT
+TACAATGATGATGATCCAGAAGATGAAGATTTCACAGAAGAAACACCAAGTTTAGAATATGATGAAGAAAACCCTGACGA
+TGAAAAATCAGAGGTAGAATCGTATGATTCTGAGATTAATGAAATCATTCCTGATGAAGATTTAGATGAGGATGTAGAAA
+TCAACGAAGAAGACGATGAAGAGGAAGAAGAGGAAGAAGAGGTTTAGACGGGGATTTTGTATTTGACAAATAGTCAGATA
+TAGTTTAAACTATTATTCGGGCACCTCTTATGAGGTCAGATAAAGCTCCCTAGTGATAGGGGGCTATTTTGTTTTTGGGA
+AAGATACAGAATGGTTCCAGATAGTTTTCTGAGTAGGCCCTTGATCAGATAGTTTCTACTAGTTTTGACTAGAGAAGCTG
+GTATTATTTATCAATCATGTGTTTTGGGTTTTACCCGTAAACTAACTGTTAGATTAACATTTAATTTAAGGAGTTTTTAA
+TGACAAAGTATATTTTTGTTACAGGTGGTGTGGTCTCTTCTATTGGTAAGGGGATTGTTGCAGCAAGTCTTGGGCGCTTA
+CTAAAAAACCGTGGGCTAAAGGTGACAATTCAAAAATTTGATCCATATATTAATATTGATCCAGGGACAATGAGCCCTTA
+TCAACATGGAGAAGTTTATGTTACAGATGATGGTGCAGAAACTGACCTTGACCTTGGACACTACGAGCGTTTTATTGATA
+TTAACTTAAACAAATATTCAAATGTTACAACGGGTAAGATTTATAGTGAAGTTCTTAAAAAAGAACGCCGTGGAGAATAC
+CTTGGTGCAACTGTTCAAGTTATCCCACACGTTACAGATGCTTTGAAAGAAAAAATCAAACGTGCTGCGACAACTACAGA
+TTCAGATGTTATTATTACTGAAGTTGGCGGTACTGTTGGAGATATTGAGAGCCTTCCGTTTTTAGAAGCACTTCGTCAAA
+TGAAGGCAGATGTTGGTTCTGATAATGTTATGTACATTCATACAACGTTATTACCATACCTAAAGGCTGCCGGCGAAATG
+AAAACAAAACCGACTCAACATTCTGTTAAAGAGTTACGTGGCCTAGGTATCCAACCTAATATGCTTGTTATCCGTACAGA
+GCAACCAGCAGGTCAAAGTATTAAGAATAAATTGGCACAATTTTGTGATGTTGCACCAGAGGCTGTTATAGAGTCCCTTG
+ACGTTGACCATATTTATCAAATTCCACTTAACATGCAAGCTCAAAATATGGATCAAATTGTTTGTGATCACTTGAAGCTT
+GAGACACCTGCTGCTGATATGACAGAATGGTCAGCAATGGTTGATAAAGTAATGAACCTTGAGAAAAAAGTTAAAATTGC
+ATTGGTTGGTAAATATGTTGAATTACCTGATGCCTACCTTTCAGTTGTGGAAGCCCTTAAGCACTCAGGGTACGTCAACG
+ATGTTGCTATTGATCTAAAATGGGTAAATGCTGCTGAAGTGACAGAAGATAATATTAAAGAACTTGTCGGAGATGCAGAT
+GGTATCATCGTTCCTGGTGGATTTGGCCAAAGAGGTAGTGAGGGTAAAATTGAAGCAATTCGCTATGCACGTGAAAATGA
+TGTTCCAATGCTTGGTGTTTGTCTCGGAATGCAGCTAACTTGTGTCGAATTTGCGCGTAATGTTTTAAACCTTCATGGAG
+CTAATTCAGCAGAGCTTGACCCTAAAACACCGTTCCCAATCATTGATATCATGCGTGATCAAATCGATATTGAAGATATG
+GGTGGTACACTTCGCCTTGGTCTATATCCATGTAAATTGAAATCAGGTTCAAGAGCTGCGGCAGCTTATAATAATCAAGA
+AGTTGTCCAACGTCGTCACCGTCACCGTTATGAATTTAATACAAAATTCCGTGAGCAATTTGAGGCTGCTGGATTTGTCT
+TCTCAGGGGTATCACCGGATAATCGTTTGATGGAAGTTGTTGAGTTACCAGAGAAAAAATTCTTTGTTGCAGCACAATAC
+CATCCAGAATTACAATCACGTCCTAACCATGCTGAAGAGCTTTACACAGCTTTTGTAACCGCAGCAGTTGAAAATATGAA
+ATAACTTTATCGCCTCCCAGTATTAGGAGGCGATTTTATTTTTTTAGATAGTTTCACTATCAAAGTATCATTAGCTCTTT
+TCTTTTTCTAAAAATAAGGTATAATAGGTTGCATGAAAAAGATTCGATTATCAAAGTTTATTAAAATGATTGTTGTTATT
+TTGTTTTTAATTAGTGTAGCAGCTAGTTTTTATTTTTTCCACGTTGCCCAAGTTCGAGATGATAAATCCTTTATTTCAAA
+TGGTCAACGTAAGCCTGGAAACTCTTTATATGCTTATGATAAATCCTTTGATAAGCTATTAAAGCAAAAAATAGAAATGA
+CAAACCAAAATATAAAGCAAGTTGCTTGGTATGTTCCTGCTGTTAAGAAAACTCATAAGACAGCTGTTGTCGTTCATGGT
+TTTGCGAATAGCAAAGAGAATATGAAGGCATATGGTTGGCTGTTTCATAAGTTAGGATACAATGTTCTTATGCCTGACAA
+TATTGCACATGGTGAAAGTCATGGGCAGTTGATAGGCTATGGCTGGAACGACCGCGAGAACATTATCAAATGGACAGAAA
+TGATAGTTGATAAGAATCCATCAAGCCAAATTACTTTATTTGGTGTTTCAATGGGTGGAGCAACAGTCATGATGGCTAGT
+GGTGAAAAATTACCTAGTCAGGTTGTTAATATCATTGAAGATTGCGGTTATTCTAGTGTTTGGGATGAATTAAAATTTCA
+GGCTAAAGAGATGTATGGTTTACCAGCCTTCCCACTCTTATATGAAGTTTCAACAATTTCTAAAATCAGAGCAGGTTTTT
+CGTATGGACAAGCAAGTAGTGTCGAACAATTGAAAAAGAATAATTTACCAGCCCTCTTTATTCATGGTGATAAGGATAAT
+TTTGTTCCAACAAGTATGGTTTATGACAACTATAAAGCTACAGCAGGTAAGAAAGAGCTTTATATTGTAAAAGGGGCAAA
+ACATGCGAAATCTTTTGAAACAGAGCCAGAAAAATATGAGAAACGTATCTCTAGTTTTTTGAAAAAATATGAAAAATAAT
+ATTGACAACAATATGATAAGTTGATATAATTTATTATGTTGTTAAGCGGGGATGGCGGAATTGGCAGACGCGCAAGACTA
+AGGATCTTGTGACCGCTTTTGGTCGTGAGGGTTCAAGTCCCTCTCTCCGCAGACTAGTCGAGTTCATTTGGAACTCGACT
+TTTTGCATATTTAAGATAAAGATGGAGTATCACATGTCAAAAGTACGTGGCTTTGAATTAGTTAGCCAATTTAGCAATAA
+AGAGTTATTACCAAAACGAGAAACAGCTCACGCAGCTGGCTATGATTTAAAAGTAGCTAAAAAAACGGTTATTGAACCTG
+GTGAAATTACATTGGTCCCGACCGGTATTAAAGCATACATGCAACCAGGGGAGGTCCTGTACCTTTATGATCGTTCATCG
+AATCCACGTAAAAAAGGGATTGTCCTAATAAATTCAGTTGGTGTTATTGATGGTGACTACTATAATAACCAAGTCAATGA
+AGGACATATTTTTGCACAGATGCAAAATATTACTGATCAGGCTGTTATTTTAGAAGAAGGGGAACGGATTGTTCAGGCTG
+TTTTTGCCCCATTCTTATTGGCAGATGACGATCAGGCTACAGGAATGCGTACAGGTGGTTTTGGTAGTACTGGAAAATAA
+AATTATTTTACGAATAATGTTAGAAAAGGCTAGACTTACTTCTTAGCCTTTTTTGATGAGAGTAAACTTATATTTTCTCT
+AACTTGGTGTGATATAATGAGTGTACTAGTTATTTGGTACCAAGCTATCATATTAATTTAGAAGTTATAAAGGAGGCCTG
+AGTGGCTAAGAAAAAATCAGTCTTCACCTGTCAAGAGTGTGGTTACCAATCACCTAAGTATTTGGGACGTTGTCCAAATT
+GCTCAGCCTGGTCTTCATTTGTAGAAGAGGTTGAAGTTCAAGAAGTTAAAAATGCACGAGTTAGTTTGAACGGTGAAAAG
+TCCCGACCGACGAAGTTAAAAGATGTTTCCTCAATTAACTATTCTAGAACTAAGACTGATATGGATGAATTTAACCGTGT
+TCTAGGAGGCGGTGTTGTACCAGGAAGTTTGGTTCTGATTGGAGGAGACCCTGGGATAGGTAAATCTACTTTATTACTAC
+AAGTATCAACTCAGCTAGCTAATAAAGGTACAGTATTATATGTCTCAGGTGAGGAATCTGCAGAACAGATTAAGTTACGA
+AGTGAGCGTCTAGGCGATATCGATAATGAATTTTACCTTTATGCCGAGACTAATATGCAAAGTATTCGGTCGGAGATTGA
+GAAGATTAAACCAGATTTTCTTATTATTGATTCTATACAAACTATTATGAGTCCCGAAGTATCAAGTGTCCAAGGCTCTG
diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
index 3bb732668c589ba07e51e9261b8e4eaeeb5137a1..2674df2b4fd4938aad6a98253d61452d80e40e18 100644
GIT binary patch
literal 115704
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zkYqxO6Y*#<ikD{g2~G<Q2KA7NTs~qF7lfM+-%O=0B8(r*!nG9{NQOx}*y?&<-ZVrq
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zu(4WYP)R)J(h$j);TAV7axPcXrupBslUX7LBBnhi%Ndlaw4-ElBD8Oc(5-6lJVE)V
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E0#w&P^8f$<


From 22e2901a8562bf1ba6f66dade49b0274ee4350f7 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 17:21:56 +0100
Subject: [PATCH 09/97] update test-data

---
 .../test-data/loci_summary_stats.tsv          | 103 ++++++++++++++++++
 tools/chewbbaca/test-data/results_alleles.tsv |   2 +
 .../test-data/results_statistics.tsv          |   2 +
 3 files changed, 107 insertions(+)
 create mode 100644 tools/chewbbaca/test-data/loci_summary_stats.tsv
 create mode 100644 tools/chewbbaca/test-data/results_alleles.tsv
 create mode 100644 tools/chewbbaca/test-data/results_statistics.tsv

diff --git a/tools/chewbbaca/test-data/loci_summary_stats.tsv b/tools/chewbbaca/test-data/loci_summary_stats.tsv
new file mode 100644
index 00000000000..9dcde38bf99
--- /dev/null
+++ b/tools/chewbbaca/test-data/loci_summary_stats.tsv
@@ -0,0 +1,103 @@
+Locus	EXC	INF	PLOT3	PLOT5	LOTSC	NIPH	NIPHEM	ALM	ASM	PAMA	LNF	Total_CDS
+GCA-000007265-protein1	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein10	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein100	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein101	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein102	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein103	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein104	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein105	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein106	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein107	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein108	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein109	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein11	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein110	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein111	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein112	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein113	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein114	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein12	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein13	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein14	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein16	0	0	0	0	0	0	1	0	0	0	0	3
+GCA-000007265-protein19	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein2	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein20	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein21	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein22	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein23	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein24	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein25	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein26	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein27	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein28	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein29	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein3	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein30	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein31	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein32	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein33	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein34	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein35	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein36	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein37	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein38	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein39	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein40	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein41	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein42	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein43	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein44	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein45	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein46	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein47	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein48	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein49	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein5	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein50	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein51	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein52	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein53	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein54	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein55	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein56	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein57	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein58	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein59	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein6	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein60	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein61	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein62	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein63	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein64	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein65	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein66	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein67	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein68	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein69	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein7	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein70	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein71	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein72	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein74	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein75	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein76	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein77	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein79	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein8	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein80	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein81	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein82	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein84	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein85	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein86	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein87	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein9	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein93	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein94	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein95	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein96	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein97	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein98	1	0	0	0	0	0	0	0	0	0	0	1
+GCA-000007265-protein99	1	0	0	0	0	0	0	0	0	0	0	1
diff --git a/tools/chewbbaca/test-data/results_alleles.tsv b/tools/chewbbaca/test-data/results_alleles.tsv
new file mode 100644
index 00000000000..4c3aa74747d
--- /dev/null
+++ b/tools/chewbbaca/test-data/results_alleles.tsv
@@ -0,0 +1,2 @@
+FILE	GCA-000007265-protein1	GCA-000007265-protein10	GCA-000007265-protein100	GCA-000007265-protein101	GCA-000007265-protein102	GCA-000007265-protein103	GCA-000007265-protein104	GCA-000007265-protein105	GCA-000007265-protein106	GCA-000007265-protein107	GCA-000007265-protein108	GCA-000007265-protein109	GCA-000007265-protein11	GCA-000007265-protein110	GCA-000007265-protein111	GCA-000007265-protein112	GCA-000007265-protein113	GCA-000007265-protein114	GCA-000007265-protein12	GCA-000007265-protein13	GCA-000007265-protein14	GCA-000007265-protein16	GCA-000007265-protein19	GCA-000007265-protein2	GCA-000007265-protein20	GCA-000007265-protein21	GCA-000007265-protein22	GCA-000007265-protein23	GCA-000007265-protein24	GCA-000007265-protein25	GCA-000007265-protein26	GCA-000007265-protein27	GCA-000007265-protein28	GCA-000007265-protein29	GCA-000007265-protein3	GCA-000007265-protein30	GCA-000007265-protein31	GCA-000007265-protein32	GCA-000007265-protein33	GCA-000007265-protein34	GCA-000007265-protein35	GCA-000007265-protein36	GCA-000007265-protein37	GCA-000007265-protein38	GCA-000007265-protein39	GCA-000007265-protein40	GCA-000007265-protein41	GCA-000007265-protein42	GCA-000007265-protein43	GCA-000007265-protein44	GCA-000007265-protein45	GCA-000007265-protein46	GCA-000007265-protein47	GCA-000007265-protein48	GCA-000007265-protein49	GCA-000007265-protein5	GCA-000007265-protein50	GCA-000007265-protein51	GCA-000007265-protein52	GCA-000007265-protein53	GCA-000007265-protein54	GCA-000007265-protein55	GCA-000007265-protein56	GCA-000007265-protein57	GCA-000007265-protein58	GCA-000007265-protein59	GCA-000007265-protein6	GCA-000007265-protein60	GCA-000007265-protein61	GCA-000007265-protein62	GCA-000007265-protein63	GCA-000007265-protein64	GCA-000007265-protein65	GCA-000007265-protein66	GCA-000007265-protein67	GCA-000007265-protein68	GCA-000007265-protein69	GCA-000007265-protein7	GCA-000007265-protein70	GCA-000007265-protein71	GCA-000007265-protein72	GCA-000007265-protein74	GCA-000007265-protein75	GCA-000007265-protein76	GCA-000007265-protein77	GCA-000007265-protein79	GCA-000007265-protein8	GCA-000007265-protein80	GCA-000007265-protein81	GCA-000007265-protein82	GCA-000007265-protein84	GCA-000007265-protein85	GCA-000007265-protein86	GCA-000007265-protein87	GCA-000007265-protein9	GCA-000007265-protein93	GCA-000007265-protein94	GCA-000007265-protein95	GCA-000007265-protein96	GCA-000007265-protein97	GCA-000007265-protein98	GCA-000007265-protein99
+GCA_000007265	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	NIPHEM	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
diff --git a/tools/chewbbaca/test-data/results_statistics.tsv b/tools/chewbbaca/test-data/results_statistics.tsv
new file mode 100644
index 00000000000..fcaedfc16f9
--- /dev/null
+++ b/tools/chewbbaca/test-data/results_statistics.tsv
@@ -0,0 +1,2 @@
+FILE	EXC	INF	PLOT3	PLOT5	LOTSC	NIPH	NIPHEM	ALM	ASM	PAMA	LNF	Invalid CDSs	Classified_CDSs	Total_CDSs
+GCA_000007265	101	0	0	0	0	0	1	0	0	0	0	10	104	114

From 698b1fd1804f76a7e8be872eb44a8ea83b413e63 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 17:29:44 +0100
Subject: [PATCH 10/97] add prepareexternalschema

---
 tools/chewbbaca/PrepExternalSchema.xml        |  24 ++++++++----------
 ...007265.1_ASM726v1_PExternalschema_seed.zip | Bin 0 -> 115704 bytes
 2 files changed, 11 insertions(+), 13 deletions(-)
 create mode 100644 tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index b36083f1f09..f5cd6957531 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -8,29 +8,26 @@
         mkdir ./schema &&
         unzip $input_schema -d ./schema &&
         chewBBACA.py PrepExternalSchema
-            #if str($advanced.training_file) != 'None'
-                --ptf '$advanced.training_file'
+            #if str($training_file) != 'None'
+                --ptf '$training_file'
             #end if            
             --bsr $blast_score_ratio
             --l $minimum_length
             --t $translation_table
             --st $size_threshold
-            #if str($advanced.size_filter) == 'true'
-                --size-filter
-            #end if
-            --size-filter $size_filter
+            $size_filter
             -g ./schema/schema_seed/ -o ./schema_seed &&
         zip -r PExternalschema_seed.zip ./schema_seed
     ]]></command>
     <inputs>
-        <param format="zip" name="input_schema" type="data" multiple="True" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <param format="zip" name="input_schema" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
-            <param argument="--training_file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--blast_score_ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
-            <param argument="--minimum_length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
-            <param argument="--translation_table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
-            <param argument="--size_threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
-            <param argument="--size-filter" type="boolean" truevalue="" falsevalue="" checked="false" label="Size filter" help="Apply the minimum length and size threshold values to filter out alleles during schema adaptation" />
+            <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
+            <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
+            <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
+            <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+            <param argument="--size-filter" type="boolean" truevalue="--size-filter" falsevalue="" checked="false" label="Size filter" help="Apply the minimum length and size threshold values to filter out alleles during schema adaptation" />
         </section>
     </inputs>
     <outputs>
@@ -39,6 +36,7 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <param name="size_filter" value="false"/>
             <output name="schema" file="GCA_000007265.1_ASM726v1_PExternalschema_seed.zip" compare="sim_size"/>
         </test>
     </tests>
diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip
new file mode 100644
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HcmV?d00001


From cbc4c7068ed4689f6cb0f7e47d468c3783959e73 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 18:01:31 +0100
Subject: [PATCH 11/97] removing uploaded wrong files

---
 tools/chewbbaca/AlleleCall.xml                |  10 +++++-----
 tools/chewbbaca/CreateSchema.xml              |   8 ++++----
 tools/chewbbaca/PrepExternalSchema.xml        |   8 ++++----
 tools/chewbbaca/macros.xml                    |  10 +---------
 ...007265.1_ASM726v1_PExternalschema_seed.zip | Bin 115704 -> 115704 bytes
 .../GCA_000007265.1_ASM726v1_schema_seed.zip  | Bin 115704 -> 115704 bytes
 6 files changed, 14 insertions(+), 22 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index d85160374e0..cae8c6365d1 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -5,12 +5,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir ./input &&
-        mkdir ./schema &&
+        mkdir './input' &&
+        mkdir './schema' &&
         #for $file in $input_file
-        cp $file ./input/${file.element_identifier} &&
+        cp $file './input/${file.element_identifier}' &&
         #end for
-        unzip $input_schema -d ./schema &&
+        unzip $input_schema -d './schema' &&
         chewBBACA.py AlleleCall
             #if str($training_file) != 'None'
                 --ptf $training_file
@@ -23,7 +23,7 @@
             --pm $prodigal_mode
             --mode $mode
             --force-continue
-            -i ./input -g ./schema/schema_seed/ -o ./output
+            -i './input' -g './schema/schema_seed/' -o './output'
     ]]></command>
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="true" label="Genome assemblies in FASTA format"/>
diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index fc665adcd98..00f063c7c26 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -5,9 +5,9 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir ./input &&
+        mkdir './input' &&
         #for $file in $input_file
-        cp $file ./input/${file.element_identifier} &&
+        ln -sf $file './input/${file.element_identifier}' &&
         #end for
         chewBBACA.py CreateSchema 
             #if str($training_file) != 'None'
@@ -18,9 +18,9 @@
             --t $translation_table
             --st $size_threshold
             --pm $prodigal_mode
-            -i ./input -o ./output &&
+            -i './input' -o './output' &&
         cd output/ &&
-        zip -r schema_seed.zip ./schema_seed
+        zip -r schema_seed.zip './schema_seed'
     ]]></command>
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index f5cd6957531..caa06b4fd46 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -5,8 +5,8 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir ./schema &&
-        unzip $input_schema -d ./schema &&
+        mkdir './schema' &&
+        unzip '$input_schema' -d './schema' &&
         chewBBACA.py PrepExternalSchema
             #if str($training_file) != 'None'
                 --ptf '$training_file'
@@ -16,8 +16,8 @@
             --t $translation_table
             --st $size_threshold
             $size_filter
-            -g ./schema/schema_seed/ -o ./schema_seed &&
-        zip -r PExternalschema_seed.zip ./schema_seed
+            -g './schema/schema_seed/' -o './schema_seed' &&
+        zip -r PExternalschema_seed.zip './schema_seed'
     ]]></command>
     <inputs>
         <param format="zip" name="input_schema" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
diff --git a/tools/chewbbaca/macros.xml b/tools/chewbbaca/macros.xml
index 4a79d108203..a72eb21a62b 100644
--- a/tools/chewbbaca/macros.xml
+++ b/tools/chewbbaca/macros.xml
@@ -12,15 +12,7 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-            @misc{githubchewBBACA,
-            author = {LastTODO, FirstTODO},
-            year = {TODO},
-            title = {chewBBACA},
-            publisher = {GitHub},
-            journal = {GitHub repository},
-            url = {https://github.com/B-UMMI/chewBBACA}
-            </citation>
+            <citation type="doi">10.1099/mgen.0.000166</citation>
         </citations>
     </xml>
 </macros>
diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip
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diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
index 2674df2b4fd4938aad6a98253d61452d80e40e18..d3801afc78eba2ab5686cca65fe9b75d1d5be462 100644
GIT binary patch
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From 5b94ea1c26bba64f19c97367fe4013d675e05363 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 19:05:13 +0100
Subject: [PATCH 12/97] aading DownloadSchema tool

---
 tools/chewbbaca/DownloadSchema.xml | 71 ++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 tools/chewbbaca/DownloadSchema.xml

diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
new file mode 100644
index 00000000000..8913e26e08c
--- /dev/null
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -0,0 +1,71 @@
+<tool id="DownloadSchema" name="chewBBACA DownloadSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Download a schema from Chewie-NS</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py DownloadSchema
+            -sp $species_id 
+            -sc $schema_id
+            -o './output' &&
+        ## The output is named based of the species name. Rename it to schema_seed so it is compatible for other chewbbaca tools.
+        mv output/* 'schema_seed' &&
+        zip -r schema_seed.zip './schema_seed'
+    ]]></command>
+    <inputs>
+        <param argument="--species-id" type="select" label="Species ID">
+            <option value="1">Streptococcus pyogenes</option>
+            <option value="2">Acinetobacter baumannii</option>
+            <option value="3">Arcobacter butzleri</option>
+            <option value="4">Campylobacter jejuni</option>
+            <option value="5">Escherichia coli</option>
+            <option value="6">Listeria monocytogenes</option>
+            <option value="7">Yersinia enterocolitica</option>
+            <option value="8">Salmonella enterica</option>
+            <option value="9">Streptococcus agalactiae</option>
+            <option value="10">Brucella melitensis</option>
+            <option value="11">Brucella melitensis</option>
+            <option value="12">Brucella melitensis</option>
+            <option value="13">Brucella melitensis</option>
+            <option value="14">Brucella melitensis</option>
+            <option value="15">Brucella melitensis</option>
+            <option value="16">Brucella melitensis</option>
+        </param>
+        <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
+        <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>
+    </inputs>
+    <outputs>
+        <data format="zip" name="schema" from_work_dir="schema_seed.zip" label="${tool.name} on ${on_string}: Schema files"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="species_id" value="13"/>
+            <param name="schema_id" value="1"/>
+            <output name="schema" file="Download_C-chauvoei_seed.zip" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+==============================
+  chewBBACA - DownloadSchema
+==============================
+
+options:
+ 
+  -sp, --species-id SPECIES_ID                     The integer identifier or name of the species
+                                                   that the schema is associated to in Chewie-NS.
+                                                   (default: None)
+                                                   
+  -sc, --schema-id SCHEMA_ID                       The URI, integer identifier or name of the schema
+                                                   to download from Chewie-NS. (default: None)
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

From cef81ada365f215098a1be3739b62374405e9eca Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 25 Mar 2024 19:06:57 +0100
Subject: [PATCH 13/97] aading DownloadSchema tool

---
 tools/chewbbaca/DownloadSchema.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
index 8913e26e08c..4489e21815f 100644
--- a/tools/chewbbaca/DownloadSchema.xml
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -25,12 +25,12 @@
             <option value="8">Salmonella enterica</option>
             <option value="9">Streptococcus agalactiae</option>
             <option value="10">Brucella melitensis</option>
-            <option value="11">Brucella melitensis</option>
-            <option value="12">Brucella melitensis</option>
-            <option value="13">Brucella melitensis</option>
-            <option value="14">Brucella melitensis</option>
-            <option value="15">Brucella melitensis</option>
-            <option value="16">Brucella melitensis</option>
+            <option value="11">Brucella</option>
+            <option value="12">Clostridium perfringens</option>
+            <option value="13">Clostridium chauvoei</option>
+            <option value="14">Bacillus anthracis</option>
+            <option value="15">Klebsiella oxytoca</option>
+            <option value="16">Clostridium neonatale</option>
         </param>
         <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
         <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>

From 74685241f81004294afd387f7111984d33525bf8 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 26 Mar 2024 12:58:45 +0100
Subject: [PATCH 14/97] Add AlleleCallEvaluator

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 tools/chewbbaca/AlleleCallEvaluator.xml

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
new file mode 100644
index 00000000000..a187029ef59
--- /dev/null
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -0,0 +1,22 @@
+<tool id="AlleleCallEvaluator" name="chewBBACA AlleleCallEvaluator" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py AlleleCallEvaluator -i AlleleCall/ -g schema_seed/ -o output/
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+        /bin/sh: 1: chewBBACA.py: not found
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

From 933f5fd738ea3d842d2ea3fa637d21045c6026c2 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 26 Mar 2024 12:59:23 +0100
Subject: [PATCH 15/97] update alleleCallEvaluator

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 26 ++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index a187029ef59..fa1ec73e717 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -1,9 +1,33 @@
-<tool id="AlleleCallEvaluator" name="chewBBACA AlleleCallEvaluator" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="AlleleCallEvaluator" name="chewBBACA AlleleCallEvaluator" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>Build an interactive report for allele calling results evaluation</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
+        mkdir './input' &&
+        mkdir './schema' &&
+        #for $file in $input_file
+        cp $file './input/${file.element_identifier}' &&
+        #end for
+        unzip $input_schema -d './schema' &&
+        chewBBACA.py AlleleCall
+            #if str($training_file) != 'None'
+                --ptf $training_file
+            #end if            
+            --bsr $blast_score_ratio
+            --l $minimum_length
+            --t $translation_table
+            --st $size_threshold
+            $no_inferred
+            --pm $prodigal_mode
+            --mode $mode
+            --force-continue
+            -i './input' -g './schema/schema_seed/' -o './output'
+
+
+
+
         chewBBACA.py AlleleCallEvaluator -i AlleleCall/ -g schema_seed/ -o output/
     ]]></command>
     <inputs>

From b7dc7c0001b7c8b640368680fd8c6a35b7563502 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 26 Mar 2024 13:01:03 +0100
Subject: [PATCH 16/97] Add FastTree requirement to macros

---
 tools/chewbbaca/macros.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/chewbbaca/macros.xml b/tools/chewbbaca/macros.xml
index a72eb21a62b..ab844c88bb1 100644
--- a/tools/chewbbaca/macros.xml
+++ b/tools/chewbbaca/macros.xml
@@ -7,6 +7,7 @@
             <requirement type="package" version="@CHEW_VERSION@">chewbbaca</requirement>
             <requirement type="package" version="2.15.0">blast</requirement>
             <requirement type="package" version="3.0">zip</requirement>
+            <requirement type="package" version="2.1.11">fasttree</requirement>
             <yield/>
         </requirements>
     </xml>

From 67a7f4c22d8c09b610d22d5d386b8f88bb499a88 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 26 Mar 2024 14:35:35 +0100
Subject: [PATCH 17/97] add AlleleCallEvaluator

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 82 +++++++++++++++++++------
 1 file changed, 64 insertions(+), 18 deletions(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index fa1ec73e717..8857fbc1cf6 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -11,35 +11,81 @@
         cp $file './input/${file.element_identifier}' &&
         #end for
         unzip $input_schema -d './schema' &&
-        chewBBACA.py AlleleCall
-            #if str($training_file) != 'None'
-                --ptf $training_file
-            #end if            
-            --bsr $blast_score_ratio
-            --l $minimum_length
-            --t $translation_table
-            --st $size_threshold
-            $no_inferred
-            --pm $prodigal_mode
-            --mode $mode
-            --force-continue
+        chewBBACA.py AlleleCallEvaluator
+            #if str($annotations) != 'None'
+                -a $annotations
+            #end if
+            $light
+            $no_pa
+            $no_dm
+            $no_tree
+            $cg_alignment
             -i './input' -g './schema/schema_seed/' -o './output'
-
-
-
-
-        chewBBACA.py AlleleCallEvaluator -i AlleleCall/ -g schema_seed/ -o output/
     ]]></command>
     <inputs>
+        <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
+        <param name="input_schema" format="zip" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <section name="advanced" title="Advanced options">
+            <param argument="--annotations" type="data" format="tabular" label="Annotation file" help="File created by the UniprotFinder module" optional="true" />
+            <param argument="--light" type="boolean" truevalue="--light" falsevalue="" checked="false" label="Do not compute the presence-absence matrix, the distance matrix  and the Neighbor-Joining tree." />
+            <param argument="--no-pa" type="boolean" truevalue="--no-pa " falsevalue="" checked="false" label="Do not compute the presence-absence matrix" />
+            <param argument="--no-dm" type="boolean" truevalue="--no-dm " falsevalue="" checked="false" label="Do not compute the distance matrix" />
+            <param argument="--no-tree" type="boolean" truevalue="--no-tree " falsevalue="" checked="false" label="Do not compute the Neighbor-Joining tree" />
+            <param argument="--cg-alignment" type="boolean" truevalue="--cg-alignment " falsevalue="" checked="false" label="Compute the MSA of the core genome loci, even if `--no-tree` is provided" />
+        </section>
     </inputs>
     <outputs>
+        <data format="html" name="allelecall_report" from_work_dir="output/allelecall_report.html" label="${tool.name} on ${on_string}: AlleleCall Report"/>
     </outputs>
     <tests>
         <test>
+            <param name="input_file">
+                <collection type="list">
+                    <element name="cds_coordinates.tsv" value="cds_coordinates.tsv" ftype="tabular"/>
+                    <element name="loci_summary_stats.tsv" value="loci_summary_stats.tsv" ftype="tabular"/>
+                    <element name="results_alleles.tsv" value="results_alleles.tsv" ftype="tabular"/>
+                    <element name="results_statistics.tsv" value="results_statistics.tsv" ftype="tabular"/>
+                </collection>
+            </param>
+            <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <output name="allelecall_report" file="allelecall_report.html" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
-        /bin/sh: 1: chewBBACA.py: not found
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+===================================
+  chewBBACA - AlleleCallEvaluator
+===================================
+
+  -i, --input-files INPUT_FILES            Path to the directory that contains the allele calling
+                                           results. (default: None)
+                                           
+  -g, --schema-directory SCHEMA_DIRECTORY  Path to the schema directory. (default: None)
+                                           
+  -o, --output-directory OUTPUT_DIRECTORY  Path to the output directory where the report HTML files
+                                           will be generated. (default: None)
+                                           
+  -a, --annotations ANNOTATIONS            Path to the TSV file created by the UniprotFinder module.
+                                           (default: None)
+                                           
+  --light                                  Do not compute the presence-absence matrix, the distance
+                                           matrix and the Neighbor-Joining tree. (default: False)
+                                           
+  --no-pa                                  Do not compute the presence-absence matrix. (default:
+                                           False)
+                                           
+  --no-dm                                  Do not compute the distance matrix. (default: False)
+                                           
+  --no-tree                                Do not compute the Neighbor-Joining tree. (default:
+                                           False)
+                                           
+  --cg-alignment                           Compute the MSA of the core genome loci, even if --no-
+                                           tree is provided. (default: False)
 
     ]]></help>
     <expand macro="citations" />

From ad1b55a10bd27b13342feb885318ab5ac9aa73c6 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 26 Mar 2024 14:36:39 +0100
Subject: [PATCH 18/97] update AlleleCall.xml to write cds_coordinates as
 output

---
 tools/chewbbaca/AlleleCall.xml                |   1 +
 tools/chewbbaca/test-data/cds_coordinates.tsv | 115 ++++++++++++++++++
 2 files changed, 116 insertions(+)
 create mode 100644 tools/chewbbaca/test-data/cds_coordinates.tsv

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index cae8c6365d1..933c62b2ea3 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -64,6 +64,7 @@
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
             <output_collection name="allelecall_results" type="list">
+                <element name="cds_coordinates" file="cds_coordinates.tsv" compare="sim_size"/>
                 <element name="loci_summary_stats" file="loci_summary_stats.tsv" compare="sim_size"/>
                 <element name="paralogous_loci" ftype="tabular">
                     <assert_contents>
diff --git a/tools/chewbbaca/test-data/cds_coordinates.tsv b/tools/chewbbaca/test-data/cds_coordinates.tsv
new file mode 100644
index 00000000000..bbb59f40af2
--- /dev/null
+++ b/tools/chewbbaca/test-data/cds_coordinates.tsv
@@ -0,0 +1,115 @@
+Genome	Contig	Start	Stop	Protein_ID	Coding_Strand
+GCA_000007265	AE009948.1	54	1463	1	1
+GCA_000007265	AE009948.1	1618	2754	2	1
+GCA_000007265	AE009948.1	2812	3705	3	1
+GCA_000007265	AE009948.1	3715	3912	4	1
+GCA_000007265	AE009948.1	4114	4317	5	1
+GCA_000007265	AE009948.1	4477	5592	6	1
+GCA_000007265	AE009948.1	5676	6251	7	1
+GCA_000007265	AE009948.1	6248	9745	8	1
+GCA_000007265	AE009948.1	10036	10308	9	1
+GCA_000007265	AE009948.1	10295	10666	10	1
+GCA_000007265	AE009948.1	10803	12089	11	1
+GCA_000007265	AE009948.1	12091	13365	12	1
+GCA_000007265	AE009948.1	13370	13912	13	1
+GCA_000007265	AE009948.1	13935	15911	14	1
+GCA_000007265	AE009948.1	17272	17466	15	-1
+GCA_000007265	AE009948.1	23103	23297	17	-1
+GCA_000007265	AE009948.1	92080	92274	88	-1
+GCA_000007265	AE009948.1	20579	20866	16	1
+GCA_000007265	AE009948.1	26410	26697	18	1
+GCA_000007265	AE009948.1	95387	95674	89	1
+GCA_000007265	AE009948.1	28902	30245	19	1
+GCA_000007265	AE009948.1	30369	31337	20	1
+GCA_000007265	AE009948.1	31334	32620	21	1
+GCA_000007265	AE009948.1	32610	33371	22	1
+GCA_000007265	AE009948.1	33434	34312	23	1
+GCA_000007265	AE009948.1	34390	35382	24	1
+GCA_000007265	AE009948.1	35393	35632	25	1
+GCA_000007265	AE009948.1	35756	36460	26	1
+GCA_000007265	AE009948.1	36583	40308	27	1
+GCA_000007265	AE009948.1	40720	42174	28	1
+GCA_000007265	AE009948.1	42202	43224	29	1
+GCA_000007265	AE009948.1	43392	43940	30	1
+GCA_000007265	AE009948.1	43963	44715	31	1
+GCA_000007265	AE009948.1	44735	46282	32	1
+GCA_000007265	AE009948.1	46475	47374	33	1
+GCA_000007265	AE009948.1	47521	48825	34	1
+GCA_000007265	AE009948.1	49072	49770	35	1
+GCA_000007265	AE009948.1	49817	51133	36	1
+GCA_000007265	AE009948.1	51221	52108	37	1
+GCA_000007265	AE009948.1	52118	52948	38	1
+GCA_000007265	AE009948.1	52961	53404	39	1
+GCA_000007265	AE009948.1	53424	54086	40	1
+GCA_000007265	AE009948.1	54083	55000	41	1
+GCA_000007265	AE009948.1	55017	55898	42	1
+GCA_000007265	AE009948.1	55906	56883	43	1
+GCA_000007265	AE009948.1	56906	57709	44	-1
+GCA_000007265	AE009948.1	57991	59256	45	1
+GCA_000007265	AE009948.1	59588	60025	46	1
+GCA_000007265	AE009948.1	60012	61103	47	1
+GCA_000007265	AE009948.1	61157	62548	48	1
+GCA_000007265	AE009948.1	62573	63871	49	1
+GCA_000007265	AE009948.1	64023	64934	50	1
+GCA_000007265	AE009948.1	65231	66229	51	1
+GCA_000007265	AE009948.1	66381	66818	52	1
+GCA_000007265	AE009948.1	66825	67205	53	1
+GCA_000007265	AE009948.1	67202	68980	54	1
+GCA_000007265	AE009948.1	69250	71892	55	1
+GCA_000007265	AE009948.1	72071	73087	56	1
+GCA_000007265	AE009948.1	73207	74697	57	1
+GCA_000007265	AE009948.1	74802	76082	58	1
+GCA_000007265	AE009948.1	76288	76596	59	1
+GCA_000007265	AE009948.1	76701	77327	60	1
+GCA_000007265	AE009948.1	77351	77974	61	1
+GCA_000007265	AE009948.1	77974	78270	62	1
+GCA_000007265	AE009948.1	78288	79121	63	1
+GCA_000007265	AE009948.1	79220	79498	64	1
+GCA_000007265	AE009948.1	79514	79858	65	1
+GCA_000007265	AE009948.1	79871	80524	66	1
+GCA_000007265	AE009948.1	80528	80941	67	1
+GCA_000007265	AE009948.1	80951	81157	68	1
+GCA_000007265	AE009948.1	81183	81443	69	1
+GCA_000007265	AE009948.1	81468	81836	70	1
+GCA_000007265	AE009948.1	81916	82221	71	1
+GCA_000007265	AE009948.1	82245	82787	72	1
+GCA_000007265	AE009948.1	82805	82990	73	1
+GCA_000007265	AE009948.1	83145	83543	74	1
+GCA_000007265	AE009948.1	83653	84189	75	1
+GCA_000007265	AE009948.1	84290	84646	76	1
+GCA_000007265	AE009948.1	84665	85159	77	1
+GCA_000007265	AE009948.1	85174	85353	78	1
+GCA_000007265	AE009948.1	85478	85918	79	1
+GCA_000007265	AE009948.1	85939	87243	80	1
+GCA_000007265	AE009948.1	87338	87976	81	1
+GCA_000007265	AE009948.1	88092	88310	82	1
+GCA_000007265	AE009948.1	88336	88452	83	1
+GCA_000007265	AE009948.1	88470	88835	84	1
+GCA_000007265	AE009948.1	88853	89236	85	1
+GCA_000007265	AE009948.1	89286	90224	86	1
+GCA_000007265	AE009948.1	90239	90625	87	1
+GCA_000007265	AE009948.1	97888	98076	90	1
+GCA_000007265	AE009948.1	98076	98246	91	1
+GCA_000007265	AE009948.1	98316	98486	92	1
+GCA_000007265	AE009948.1	98822	99082	93	-1
+GCA_000007265	AE009948.1	99401	99952	94	1
+GCA_000007265	AE009948.1	100172	100591	95	1
+GCA_000007265	AE009948.1	100791	101270	96	1
+GCA_000007265	AE009948.1	101392	102084	97	1
+GCA_000007265	AE009948.1	102081	102833	98	1
+GCA_000007265	AE009948.1	102830	103405	99	1
+GCA_000007265	AE009948.1	103548	104582	100	1
+GCA_000007265	AE009948.1	104624	105157	101	1
+GCA_000007265	AE009948.1	105338	107167	102	1
+GCA_000007265	AE009948.1	107456	108595	103	1
+GCA_000007265	AE009948.1	108709	109956	104	1
+GCA_000007265	AE009948.1	110027	110803	105	1
+GCA_000007265	AE009948.1	110766	111524	106	1
+GCA_000007265	AE009948.1	111534	111998	107	1
+GCA_000007265	AE009948.1	111995	112564	108	1
+GCA_000007265	AE009948.1	112601	113443	109	-1
+GCA_000007265	AE009948.1	113600	114883	110	1
+GCA_000007265	AE009948.1	115072	115647	111	1
+GCA_000007265	AE009948.1	115920	117524	112	1
+GCA_000007265	AE009948.1	117633	118559	113	1
+GCA_000007265	AE009948.1	118754	119200	114	1

From 0256df7ba12af3a85a2435324ef51ef1771eaa1b Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 26 Mar 2024 16:11:26 +0100
Subject: [PATCH 19/97] Update AllelCallEvluator

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 8857fbc1cf6..fb012e5f032 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -20,7 +20,8 @@
             $no_dm
             $no_tree
             $cg_alignment
-            -i './input' -g './schema/schema_seed/' -o './output'
+            -i './input' -g './schema/schema_seed/' -o '${allelecall_report.files_path}' &&
+        cp '${allelecall_report.files_path}'/allelecall_report.html $allelecall_report
     ]]></command>
     <inputs>
         <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
@@ -35,7 +36,7 @@
         </section>
     </inputs>
     <outputs>
-        <data format="html" name="allelecall_report" from_work_dir="output/allelecall_report.html" label="${tool.name} on ${on_string}: AlleleCall Report"/>
+        <data format="html" name="allelecall_report" label="${tool.name} on ${on_string}: AlleleCall Report"/>
     </outputs>
     <tests>
         <test>

From 0ca96db453e05f97e9cb824e2d13f2922b93f9a6 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 26 Mar 2024 16:11:56 +0100
Subject: [PATCH 20/97] update test.data

---
 ...007265.1_ASM726v1_PExternalschema_seed.zip | Bin 115704 -> 115704 bytes
 .../GCA_000007265.1_ASM726v1_schema_seed.zip  | Bin 115704 -> 115704 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip
index c3c871fdc4420f7d131c28a99b50589bfa651a95..45f648373f3f9dd9eff3db1d6e41812d59e3e905 100644
GIT binary patch
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diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
index d3801afc78eba2ab5686cca65fe9b75d1d5be462..db98224cbfc5b1996b3205b294bcaa9235f0e1da 100644
GIT binary patch
delta 9195
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delta 9195
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From 1092358102b24b1a72a98e273fab8f0101c03eac Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 26 Mar 2024 16:14:03 +0100
Subject: [PATCH 21/97] update test-data

---
 tools/chewbbaca/test-data/allelecall_report.html | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 tools/chewbbaca/test-data/allelecall_report.html

diff --git a/tools/chewbbaca/test-data/allelecall_report.html b/tools/chewbbaca/test-data/allelecall_report.html
new file mode 100644
index 00000000000..6e7b82c45e2
--- /dev/null
+++ b/tools/chewbbaca/test-data/allelecall_report.html
@@ -0,0 +1,16 @@
+
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>AlleleCall Report - React Edition</title>
+</head>
+<body style="background-color: #f6f6f6">
+    <noscript> You need to enable JavaScript to run this app. </noscript>
+    <div id="root"></div>
+    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", 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101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 10, 104, 114]]}], "loci_stats": [{"columns": ["Locus", "Total CDSs", "Valid Classes", "Invalid Classes", "Proportion Samples", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [["GCA-000007265-protein1", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein58", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein67", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein66", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein65", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein64", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein63", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein62", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein61", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein60", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein6", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein59", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein57", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein69", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein56", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein55", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein54", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein53", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein52", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein51", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein50", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein5", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein49", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein48", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein68", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein7", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein10", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein84", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein98", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein97", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein96", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein95", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein94", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein93", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein9", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein87", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein86", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein85", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein82", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein70", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein81", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein80", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein8", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein79", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein77", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein76", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein75", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein74", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein72", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein71", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein47", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein46", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein45", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein44", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein2", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein19", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein14", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein13", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein12", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein114", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein113", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein112", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein111", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein110", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein11", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein109", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein108", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein107", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein106", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein105", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein104", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein103", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein102", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein101", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein100", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein20", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein21", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein22", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein33", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein43", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein42", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein41", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein40", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein39", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein38", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein37", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein36", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein35", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein34", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein32", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein23", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein31", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein30", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein3", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein29", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein28", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein27", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein26", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein25", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein24", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein99", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein16", 3, 0, 1, 0.0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "annotations": [{"columns": []}, {"rows": []}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265:0.000000000);\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>
+    <script src="./report_bundle.js"></script>
+</body>
+</html>
+

From 0bd6e4f025b93b363f7340c40445b692aa5407cf Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 11:21:38 +0100
Subject: [PATCH 22/97] add ExtractCgMLST.xml

---
 tools/chewbbaca/ExtractCgMLST.xml | 71 +++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 tools/chewbbaca/ExtractCgMLST.xml

diff --git a/tools/chewbbaca/ExtractCgMLST.xml b/tools/chewbbaca/ExtractCgMLST.xml
new file mode 100644
index 00000000000..c20f609c4ff
--- /dev/null
+++ b/tools/chewbbaca/ExtractCgMLST.xml
@@ -0,0 +1,71 @@
+<tool id="ExtractCgMLST" name="chewBBACA ExtractCgMLST" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>Determine the set of loci that constitute the core genome</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir './input' &&
+        #for $file in $input_file
+        cp $file './input/${file.element_identifier}' &&
+        #end for
+        chewBBACA.py ExtractCgMLST
+        --t $threshold
+        #if str($genes2remove) != 'false'
+            --r './input/paralogous_counts.tsv'
+        #end if 
+        #if str($genomes2remove) != 'None'
+            --g $genomes2remove
+        #end if 
+        -i './input/results_alleles.tsv' -o './output' &&
+    zip -r ExtractCgMLST.zip './output'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
+        <section name="advanced" title="Advanced options">
+            <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/>
+            <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values">
+                <validator type="regex">[ .0-9]+</validator>
+            </param>
+            <param name="genes2remove" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove paralogous counts?" help="--genes2remove"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="zip" name="ExtractCgMLST" from_work_dir="ExtractCgMLST.zip" label="${tool.name} on ${on_string}: ExtractCgMLST files"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file">
+                <collection type="list">
+                    <element name="results_alleles.tsv" value="results_alleles.tsv" ftype="tabular"/>
+                </collection>
+            </param>
+            <output name="ExtractCgMLST" file="ExtractCgMLST.zip" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+=============================
+  chewBBACA - ExtractCgMLST
+=============================
+  --t, --threshold THRESHOLD [THRESHOLD ...]  Genes that constitute the core genome must be in a
+                                              proportion of genomes that is at least equal to this
+                                              value. Users can provide multiple values. (default:
+                                              [0.95, 0.99, 1])
+
+  --r, --genes2remove GENES2REMOVE            Path to file with a list of genes/columns to remove
+                                              from the matrix (one gene identifier per line).
+                                              (default: False)
+                                              
+  --g, --genomes2remove GENOMES2REMOVE        Path to file with a list of genomes/rows to remove
+                                              from the matrix (one genome identifier per line).
+                                              (default: False)
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

From 422a8a2c8479c2a20d6eaf67eee53ce7584b8c2a Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 13:21:42 +0100
Subject: [PATCH 23/97] add NSStats.xml

---
 tools/chewbbaca/NSStats.xml | 82 +++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 tools/chewbbaca/NSStats.xml

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
new file mode 100644
index 00000000000..2cca9609814
--- /dev/null
+++ b/tools/chewbbaca/NSStats.xml
@@ -0,0 +1,82 @@
+<tool id="NSStats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>Retrieve basic information about the species and schemas in Chewie-NS</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py NSStats
+            -m $mode
+            --sp $species_id 
+            --sc $schema_id
+            --ns $nomenclature_server > NSStats.txt
+    ]]></command>
+    <inputs>
+        <param argument="mode" type="select" label="Mode">
+            <option value="species">species: </option>
+            <option value="schemas">schemas: </option>
+        </param>
+        <param argument="--species-id" type="select" label="Species ID">
+            <option value="1">Streptococcus pyogenes</option>
+            <option value="2">Acinetobacter baumannii</option>
+            <option value="3">Arcobacter butzleri</option>
+            <option value="4">Campylobacter jejuni</option>
+            <option value="5">Escherichia coli</option>
+            <option value="6">Listeria monocytogenes</option>
+            <option value="7">Yersinia enterocolitica</option>
+            <option value="8">Salmonella enterica</option>
+            <option value="9">Streptococcus agalactiae</option>
+            <option value="10">Brucella melitensis</option>
+            <option value="11">Brucella</option>
+            <option value="12">Clostridium perfringens</option>
+            <option value="13">Clostridium chauvoei</option>
+            <option value="14">Bacillus anthracis</option>
+            <option value="15">Klebsiella oxytoca</option>
+            <option value="16">Clostridium neonatale</option>
+        </param>
+        <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
+        <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>
+        <param argument="--nomenclature-server" type="select" label="nomenclature server" >
+            <option value="main" selected="true">main "https://chewbbaca.online/"</option>
+            <option value="tutorial">tutorial "https://tutorial.chewbbaca.online/"</option>
+            <option value="local">local "http://127.0.0.1:5000/NS/api/"</option>                
+        </param>
+    </inputs>
+    <outputs>
+        <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name} on ${on_string}: NSStats"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="mode" value="species" />
+            <output name="NSStats" file="NSStats.txt" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+  -m, --mode {species,schemas}                     The process can retrieve the list of species
+                                                   ("species" option) in Chewie-NS or the list of
+                                                   schemas for a species ("schemas" option).
+                                                   (default: None)
+                                                   
+  --sp, --species-id SPECIES_ID                    The integer identifier of a species in Chewie-NS.
+                                                   (default: None)
+                                                   
+  --sc, --schema-id SCHEMA_ID                      The integer identifier of a schema in Chewie-NS.
+                                                   (default: None)
+                                                   
+  --ns, --nomenclature-server NOMENCLATURE_SERVER  The base URL for the Chewie-NS instance. The
+                                                   default value, "main", will establish a
+                                                   connection to "https://chewbbaca.online/",
+                                                   "tutorial" to
+                                                   "https://tutorial.chewbbaca.online/" and "local"
+                                                   to "http://127.0.0.1:5000/NS/api/" (localhost).
+                                                   Users may also provide the IP address to other
+                                                   Chewie-NS instances. (default: main)
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

From 9d1dc78e43be71916ad82c56888e17f78cb7a67f Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 13:51:57 +0100
Subject: [PATCH 24/97] add JoinProfiles.xml

---
 tools/chewbbaca/JoinProfiles.xml | 43 ++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 tools/chewbbaca/JoinProfiles.xml

diff --git a/tools/chewbbaca/JoinProfiles.xml b/tools/chewbbaca/JoinProfiles.xml
new file mode 100644
index 00000000000..c6f7413eec2
--- /dev/null
+++ b/tools/chewbbaca/JoinProfiles.xml
@@ -0,0 +1,43 @@
+<tool id="JoinProfiles" name="chewBBACA JoinProfiles" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>Join allele calling results from different runs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[      
+        chewBBACA.py JoinProfiles
+            -p $input1
+            #for $q in $queries 
+                '${q.input2}'
+            #end for
+            -o JoinedProfile.tsv
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="tsv" multiple="false" label="AlleleCall results" />
+        <repeat name="queries" title="AlleleCall results to join">
+            <param name="input2" type="data" format="tsv" label="Select"/>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="tsv" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="results_alleles.tsv"/>
+            <param name="input2" value="results_alleles.tsv"/>
+            <output name="JoinedProfile" file="JoinedProfile.tsv" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+============================
+  chewBBACA - JoinProfiles
+============================
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

From d867846ac3e98018a4e1046520228342665b48f7 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 13:53:07 +0100
Subject: [PATCH 25/97] updata test-data

---
 ...007265.1_ASM726v1_PExternalschema_seed.zip | Bin 115704 -> 115704 bytes
 .../GCA_000007265.1_ASM726v1_schema_seed.zip  | Bin 115704 -> 115704 bytes
 tools/chewbbaca/test-data/JoinedProfile.tsv   |   3 ++
 tools/chewbbaca/test-data/NSStats.txt         |  39 ++++++++++++++++++
 4 files changed, 42 insertions(+)
 create mode 100644 tools/chewbbaca/test-data/JoinedProfile.tsv
 create mode 100644 tools/chewbbaca/test-data/NSStats.txt

diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip
index 45f648373f3f9dd9eff3db1d6e41812d59e3e905..dcee05e373222b00502dccbd34deef6a9b8014fb 100644
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diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
index db98224cbfc5b1996b3205b294bcaa9235f0e1da..e49bf9d3022d5ac9174112a1f0b3ad2f18ee39f5 100644
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zB{3@@IWLhxxoEhp)yZ6F)h`c{!+Fpu7(>k-iTJI8no@~)tcIFmiMXyoF}6A9uYp$1
z1d?otG|z{cB@+2dBC`u%^gjxqpQJA#xh;`Ng;4X0L`D@s%|(d}Sqn9%CGz1qnDg;<
z&?<aAB>N@O^DC$+mq@o_s3|FitHpf-)D%gi-Pcf)ClT{Ts97!%`%O?YPa;nwGGjBe
zy0;mQBEAGx^+pM_irWH7-4<vyY%A1!FOjHi(5hw|wCY<5Nwq|Rx5H8F-VUvNcfeSs
zJD|p6CnUu?p;gCSP?Nt4MsHIFNoE<eGL=KJNFslhTSce;EB)}>u7SDa@Lu!^SychM
zpN0zPa+(6k|0FVDw^a~&3}4#~tz!2;a$yg&8d3>0rzP^C1#12!kv@B&W}id?s-UJ!
zB3<`E&1Q+X?}wTqiL^TaM~WrV`XHR}^n=i|@euU0KqAi%L966yNFGRJ%3-Ma?_qJj
evKQm9BanO}k$|I6vr!_>$Dn4BPQE{eJpKkaUbBY)

diff --git a/tools/chewbbaca/test-data/JoinedProfile.tsv b/tools/chewbbaca/test-data/JoinedProfile.tsv
new file mode 100644
index 00000000000..1fb31f9da4f
--- /dev/null
+++ b/tools/chewbbaca/test-data/JoinedProfile.tsv
@@ -0,0 +1,3 @@
+FILE	GCA-000007265-protein1	GCA-000007265-protein10	GCA-000007265-protein100	GCA-000007265-protein101	GCA-000007265-protein102	GCA-000007265-protein103	GCA-000007265-protein104	GCA-000007265-protein105	GCA-000007265-protein106	GCA-000007265-protein107	GCA-000007265-protein108	GCA-000007265-protein109	GCA-000007265-protein11	GCA-000007265-protein110	GCA-000007265-protein111	GCA-000007265-protein112	GCA-000007265-protein113	GCA-000007265-protein114	GCA-000007265-protein12	GCA-000007265-protein13	GCA-000007265-protein14	GCA-000007265-protein16	GCA-000007265-protein19	GCA-000007265-protein2	GCA-000007265-protein20	GCA-000007265-protein21	GCA-000007265-protein22	GCA-000007265-protein23	GCA-000007265-protein24	GCA-000007265-protein25	GCA-000007265-protein26	GCA-000007265-protein27	GCA-000007265-protein28	GCA-000007265-protein29	GCA-000007265-protein3	GCA-000007265-protein30	GCA-000007265-protein31	GCA-000007265-protein32	GCA-000007265-protein33	GCA-000007265-protein34	GCA-000007265-protein35	GCA-000007265-protein36	GCA-000007265-protein37	GCA-000007265-protein38	GCA-000007265-protein39	GCA-000007265-protein40	GCA-000007265-protein41	GCA-000007265-protein42	GCA-000007265-protein43	GCA-000007265-protein44	GCA-000007265-protein45	GCA-000007265-protein46	GCA-000007265-protein47	GCA-000007265-protein48	GCA-000007265-protein49	GCA-000007265-protein5	GCA-000007265-protein50	GCA-000007265-protein51	GCA-000007265-protein52	GCA-000007265-protein53	GCA-000007265-protein54	GCA-000007265-protein55	GCA-000007265-protein56	GCA-000007265-protein57	GCA-000007265-protein58	GCA-000007265-protein59	GCA-000007265-protein6	GCA-000007265-protein60	GCA-000007265-protein61	GCA-000007265-protein62	GCA-000007265-protein63	GCA-000007265-protein64	GCA-000007265-protein65	GCA-000007265-protein66	GCA-000007265-protein67	GCA-000007265-protein68	GCA-000007265-protein69	GCA-000007265-protein7	GCA-000007265-protein70	GCA-000007265-protein71	GCA-000007265-protein72	GCA-000007265-protein74	GCA-000007265-protein75	GCA-000007265-protein76	GCA-000007265-protein77	GCA-000007265-protein79	GCA-000007265-protein8	GCA-000007265-protein80	GCA-000007265-protein81	GCA-000007265-protein82	GCA-000007265-protein84	GCA-000007265-protein85	GCA-000007265-protein86	GCA-000007265-protein87	GCA-000007265-protein9	GCA-000007265-protein93	GCA-000007265-protein94	GCA-000007265-protein95	GCA-000007265-protein96	GCA-000007265-protein97	GCA-000007265-protein98	GCA-000007265-protein99
+GCA_000007265	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	NIPHEM	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
+GCA_000007265	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	NIPHEM	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
diff --git a/tools/chewbbaca/test-data/NSStats.txt b/tools/chewbbaca/test-data/NSStats.txt
new file mode 100644
index 00000000000..f3ab4c805c0
--- /dev/null
+++ b/tools/chewbbaca/test-data/NSStats.txt
@@ -0,0 +1,39 @@
+
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+=======================
+  chewBBACA - NSStats
+=======================
+Started at: 2024-03-27T12:17:56
+
+
+Retrieving data...
+
+------------------------------------------------------------------------------
+Species                             id       #schemas     #loci      #alleles 
+------------------------------------------------------------------------------
+Streptococcus pyogenes              1           1          3044       398511  
+Acinetobacter baumannii             2           1          2390       701606  
+Arcobacter butzleri                 3           1          7474       82419   
+Campylobacter jejuni                4           1          2794       299214  
+Escherichia coli                    5           1          7601      2963736  
+Listeria monocytogenes              6           1          1748       371020  
+Yersinia enterocolitica             7           1          6344       154555  
+Salmonella enterica                 8           1          8558      2879459  
+Streptococcus agalactiae            9           1          3641       248987  
+Brucella melitensis                 10          1          2762       11222   
+Brucella                            11          1          1764       78557   
+Clostridium perfringens             12          1          1431       152324  
+Clostridium chauvoei                13          1          2223        7711   
+Bacillus anthracis                  14          1          3803       52474   
+Klebsiella oxytoca                  15          1          4201       132939  
+Clostridium neonatale               16          1          2350       13115   
+------------------------------------------------------------------------------
+
+
+Finished at: 2024-03-27T12:18:00
+Took  0m 4s.

From 7fe39d56dadfb4fcbc272a8bc57f01ba1df533b6 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 14:52:38 +0100
Subject: [PATCH 26/97] final NSStats.xml

---
 tools/chewbbaca/NSStats.xml           | 41 +++++++--------------------
 tools/chewbbaca/test-data/NSStats.txt |  4 +--
 2 files changed, 12 insertions(+), 33 deletions(-)

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index 2cca9609814..1a27362800e 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -1,4 +1,4 @@
-<tool id="NSStats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="NSStats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Retrieve basic information about the species and schemas in Chewie-NS</description>
     <macros>
         <import>macros.xml</import>
@@ -12,11 +12,11 @@
             --ns $nomenclature_server > NSStats.txt
     ]]></command>
     <inputs>
-        <param argument="mode" type="select" label="Mode">
+        <param argument="mode" type="select" label="Mode" optional="false">
             <option value="species">species: </option>
             <option value="schemas">schemas: </option>
         </param>
-        <param argument="--species-id" type="select" label="Species ID">
+        <param argument="--species-id" type="select" label="Species ID" optional="true">
             <option value="1">Streptococcus pyogenes</option>
             <option value="2">Acinetobacter baumannii</option>
             <option value="3">Arcobacter butzleri</option>
@@ -35,8 +35,8 @@
             <option value="16">Clostridium neonatale</option>
         </param>
         <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
-        <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>
-        <param argument="--nomenclature-server" type="select" label="nomenclature server" >
+        <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID" optional="true"/>
+        <param argument="--nomenclature-server" type="select" label="nomenclature server" optional="false">
             <option value="main" selected="true">main "https://chewbbaca.online/"</option>
             <option value="tutorial">tutorial "https://tutorial.chewbbaca.online/"</option>
             <option value="local">local "http://127.0.0.1:5000/NS/api/"</option>                
@@ -51,32 +51,11 @@
             <output name="NSStats" file="NSStats.txt" compare="sim_size" />
         </test>
     </tests>
-    <help><![CDATA[
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
-  -m, --mode {species,schemas}                     The process can retrieve the list of species
-                                                   ("species" option) in Chewie-NS or the list of
-                                                   schemas for a species ("schemas" option).
-                                                   (default: None)
-                                                   
-  --sp, --species-id SPECIES_ID                    The integer identifier of a species in Chewie-NS.
-                                                   (default: None)
-                                                   
-  --sc, --schema-id SCHEMA_ID                      The integer identifier of a schema in Chewie-NS.
-                                                   (default: None)
-                                                   
-  --ns, --nomenclature-server NOMENCLATURE_SERVER  The base URL for the Chewie-NS instance. The
-                                                   default value, "main", will establish a
-                                                   connection to "https://chewbbaca.online/",
-                                                   "tutorial" to
-                                                   "https://tutorial.chewbbaca.online/" and "local"
-                                                   to "http://127.0.0.1:5000/NS/api/" (localhost).
-                                                   Users may also provide the IP address to other
-                                                   Chewie-NS instances. (default: main)
-    ]]></help>
+The NSStats module enables the retrieval of information from the Chewie-NS server. Its main objective is to provide information about the list of species and schemas in Chewie-NS, so that users can quickly identify a schema of interest and download it.
+
+    </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file
diff --git a/tools/chewbbaca/test-data/NSStats.txt b/tools/chewbbaca/test-data/NSStats.txt
index f3ab4c805c0..8372b0424fa 100644
--- a/tools/chewbbaca/test-data/NSStats.txt
+++ b/tools/chewbbaca/test-data/NSStats.txt
@@ -8,7 +8,7 @@ Contacts: imm-bioinfo@medicina.ulisboa.pt
 =======================
   chewBBACA - NSStats
 =======================
-Started at: 2024-03-27T12:17:56
+Started at: 2024-03-27T13:51:03
 
 
 Retrieving data...
@@ -35,5 +35,5 @@ Clostridium neonatale               16          1          2350       13115
 ------------------------------------------------------------------------------
 
 
-Finished at: 2024-03-27T12:18:00
+Finished at: 2024-03-27T13:51:07
 Took  0m 4s.

From d67b1b72d24255f41c0bb2896bdd19ad009422ca Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 15:31:41 +0100
Subject: [PATCH 27/97] Final NSStats.xml with help

---
 tools/chewbbaca/NSStats.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index 1a27362800e..4bb6e676db4 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -12,7 +12,7 @@
             --ns $nomenclature_server > NSStats.txt
     ]]></command>
     <inputs>
-        <param argument="mode" type="select" label="Mode" optional="false">
+        <param argument="--mode" type="select" label="Mode" optional="false">
             <option value="species">species: </option>
             <option value="schemas">schemas: </option>
         </param>
@@ -43,7 +43,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name} on ${on_string}: NSStats"/>
+        <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name}"/>
     </outputs>
     <tests>
         <test>

From 2a34a6ad45469d1063cdc4922a7ad6f8dc5b059b Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 15:46:43 +0100
Subject: [PATCH 28/97] final DownloadSchema.xml

---
 tools/chewbbaca/DownloadSchema.xml | 36 ++++++++++++++----------------
 1 file changed, 17 insertions(+), 19 deletions(-)

diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
index 4489e21815f..d517073941c 100644
--- a/tools/chewbbaca/DownloadSchema.xml
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -9,7 +9,7 @@
             -sp $species_id 
             -sc $schema_id
             -o './output' &&
-        ## The output is named based of the species name. Rename it to schema_seed so it is compatible for other chewbbaca tools.
+        ## The output is named based on the species name. Rename it to schema_seed so it is compatible for other chewbbaca tools.
         mv output/* 'schema_seed' &&
         zip -r schema_seed.zip './schema_seed'
     ]]></command>
@@ -36,7 +36,7 @@
         <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>
     </inputs>
     <outputs>
-        <data format="zip" name="schema" from_work_dir="schema_seed.zip" label="${tool.name} on ${on_string}: Schema files"/>
+        <data format="zip" name="schema" from_work_dir="schema_seed.zip" label="${tool.name} Schema files"/>
     </outputs>
     <tests>
         <test>
@@ -46,26 +46,24 @@
         </test>
     </tests>
     <help><![CDATA[
-        
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
-==============================
-  chewBBACA - DownloadSchema
-==============================
+The DownloadSchema module enables the download of schemas from the Chewie-NS server.
 
-options:
- 
-  -sp, --species-id SPECIES_ID                     The integer identifier or name of the species
-                                                   that the schema is associated to in Chewie-NS.
-                                                   (default: None)
-                                                   
-  -sc, --schema-id SCHEMA_ID                       The URI, integer identifier or name of the schema
-                                                   to download from Chewie-NS. (default: None)
+.. class:: infomark 
+**Note**
 
+The output schema files are in a zip file. This file can be used as input for other chewBBACA tools.
+
+-----
+
+Compressed versions of every schema in the Chewie-NS are also available for download:
+ - through the `Chewie-NS public website`_
+ - through the (/species/{species_id}/schemas/{schema_id}/zip) API endpoint in Swagger_
+ - with a simple curl command (e.g.: curl -X GET "https://chewbbaca.online/NS/api/species/9/schemas/1/zip?request_type=download" -H  "accept: application/json")
+
+.. _Chewie-NS public website: https://chewbbaca.online/
+.. _Swagger: https://chewbbaca.online/api/NS/api/docs
     ]]></help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From c97a0c02e17b2585849a128c2759d8995690dfc7 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 15:57:41 +0100
Subject: [PATCH 29/97] final DownloadSchema with help and a little correction
 to NSStema.xml

---
 tools/chewbbaca/DownloadSchema.xml | 11 +++++++++--
 tools/chewbbaca/NSStats.xml        |  2 +-
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
index d517073941c..b6b3fb22ad7 100644
--- a/tools/chewbbaca/DownloadSchema.xml
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -34,6 +34,11 @@
         </param>
         <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
         <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>
+        <param argument="--nomenclature-server" type="select" label="Nomenclature server" optional="false">
+            <option value="main" selected="true">main "https://chewbbaca.online/"</option>
+            <option value="tutorial">tutorial "https://tutorial.chewbbaca.online/"</option>
+            <option value="local">local "http://127.0.0.1:5000/NS/api/"</option>                
+        </param>
     </inputs>
     <outputs>
         <data format="zip" name="schema" from_work_dir="schema_seed.zip" label="${tool.name} Schema files"/>
@@ -45,12 +50,14 @@
             <output name="schema" file="Download_C-chauvoei_seed.zip" compare="sim_size"/>
         </test>
     </tests>
-    <help><![CDATA[
+    <help>
 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
 The DownloadSchema module enables the download of schemas from the Chewie-NS server.
 
+
 .. class:: infomark 
+
 **Note**
 
 The output schema files are in a zip file. This file can be used as input for other chewBBACA tools.
@@ -64,6 +71,6 @@ Compressed versions of every schema in the Chewie-NS are also available for down
 
 .. _Chewie-NS public website: https://chewbbaca.online/
 .. _Swagger: https://chewbbaca.online/api/NS/api/docs
-    ]]></help>
+    </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file
diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index 4bb6e676db4..cb573d72e11 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -36,7 +36,7 @@
         </param>
         <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
         <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID" optional="true"/>
-        <param argument="--nomenclature-server" type="select" label="nomenclature server" optional="false">
+        <param argument="--nomenclature-server" type="select" label="Nomenclature server" optional="false">
             <option value="main" selected="true">main "https://chewbbaca.online/"</option>
             <option value="tutorial">tutorial "https://tutorial.chewbbaca.online/"</option>
             <option value="local">local "http://127.0.0.1:5000/NS/api/"</option>                

From 15007cd8e78fbe19329c99992348801c79eb1822 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 16:13:20 +0100
Subject: [PATCH 30/97] final CreatSchema.xml with help

---
 tools/chewbbaca/CreateSchema.xml | 70 +++++++++-----------------------
 1 file changed, 19 insertions(+), 51 deletions(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 00f063c7c26..ad6b0304644 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -46,7 +46,7 @@
     </inputs>
     <outputs>
         <data format="zip" name="schema" from_work_dir="output/schema_seed.zip" label="${tool.name} on ${on_string}: Schema files"/>
-        <data format="txt" name="txt_file" from_work_dir="output/invalid_cds.txt" label="${tool.name} on ${on_string}: invalid CDS">
+        <data format="txt" name="txt_file" from_work_dir="output/invalid_cds.txt" label="${tool.name} on ${on_string}: Invalid CDS">
             <filter>output['show_cds_invalid']</filter>
         </data>
         <data format="tsv" name="tst_file" from_work_dir="output/cds_coordinates.tsv" label="${tool.name} on ${on_string}: CDS coordinates">
@@ -59,61 +59,29 @@
         <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip" compare="sim_size"/>
         </test>
     </tests>
-    <help><![CDATA[
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
-============================
-chewBBACA - CreateSchema
-============================
-usage: 
-Create schema from genome assemblies.
+A Schema is a pre-defined set of loci that is used in MLST analyses. Traditional MLST schemas relied in 7 loci that were internal fragments of housekeeping genes and each locus was defined by its amplification by a pair of primers yielding a fragment of a defined size.
 
-positional arguments:
-CreateSchema
+In genomic analyses, schemas are a set of loci that are:
 
-options:
+- Present in the majority of strains for core genome (cg) MLST schemas, typically a threshold of presence in 95% of the strains is used in schema creation. The assumption is that in each strain up to 5% of loci may not be identified due to sequencing coverage problems, assembly problems or other issues related to the use of draft genome assemblies.
+- Present in at least one of the analyzed strains in the schema creation for pan genome/whole genome (pg/wg) MLST schemas.
+- Present in less than 95% of the strains for accessory genome (ag) MLST schemas.
 
--i, --input-files [INPUT_FILES]               Path to the directory that contains the input FASTA
-                                                files. Alternatively, a file with a list of full
-                                                paths to FASTA files, one per line. (default: None)
-                                                
--o, --output-directory OUTPUT_DIRECTORY       Output directory where the process will store
-                                                intermediate files and create the schema's
-                                                directory. (default: None)
-                                                
---ptf, --training-file PTF_PATH               Path to the Prodigal training file. (default: None)
-                                                
---bsr, --blast-score-ratio BLAST_SCORE_RATIO  BLAST Score Ratio value. Sequences with alignments
-                                                with a BSR value equal to or greater than this value
-                                                will be considered as sequences from the same gene.
-                                                (default: 0.6)
-                                                
---l, --minimum-length MINIMUM_LENGTH          Minimum sequence length value. Coding sequences
-                                                shorter than this value are excluded. (default: 201)
-                                                
---t, --translation-table TRANSLATION_TABLE    Genetic code used to predict genes and to translate
-                                                coding sequences. (default: 11)
-                                                
---st, --size-threshold SIZE_THRESHOLD         CDS size variation threshold. Added to the schema's
-                                                config file and used to identify alleles with a
-                                                length value that deviates from the locus length
-                                                mode during the allele calling process. (default:
-                                                0.2)
-                                                
---pm, --prodigal-mode {single,meta}           Prodigal running mode ("single" for finished
-                                                genomes, reasonable quality draft genomes and big
-                                                viruses. "meta" for metagenomes, low quality draft
-                                                genomes, small viruses, and small plasmids).
-                                                (default: single)
-                                                
+.. class:: infomark 
+
+**Note**
+
+These definitions are always operational in nature, in the sense that the analyses are performed on a limited number of strains representing part of the biological diversity of a given species or genus and are always dependent on the definition of thresholds.
+
+.. class:: infomark
+
+**Important**
+
+The use of a prodigal training file for schema creation is highly recommended.
 
-It is strongly advised to provide a training file to create a schema. Module documentation available
-at https://chewbbaca.readthedocs.io/en/latest/user/modules/CreateSchema.html
-        ]]>
     </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From 2d5f9155f7b877a33d23cade5918cb53098b9a1e Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 16:29:42 +0100
Subject: [PATCH 31/97] final PrepExternalSchema.xml with help

---
 tools/chewbbaca/PrepExternalSchema.xml | 27 ++++++++------------------
 1 file changed, 8 insertions(+), 19 deletions(-)

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index caa06b4fd46..18a7193a2f4 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -20,7 +20,7 @@
         zip -r PExternalschema_seed.zip './schema_seed'
     ]]></command>
     <inputs>
-        <param format="zip" name="input_schema" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
             <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
@@ -40,28 +40,17 @@
             <output name="schema" file="GCA_000007265.1_ASM726v1_PExternalschema_seed.zip" compare="sim_size"/>
         </test>
     </tests>
-    <help><![CDATA[
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
-        --ptf, --training-file     (Optional) Path to the Prodigal training file that will be included in
-                                the adapted schema (default: None).
+The PrepExternalSchema module enables the adaptation of external schemas so that it is possible to use those schemas with chewBBACA.
 
-        --bsr, --blast-score-ratio (Optional) The BLAST Score Ratio value that will be used to adapt
-                                the external schema (default: 0.6).
+.. class:: infomark
 
-        --l, --minimum-length      (Optional) Minimum sequence length accepted. Sequences with a length
-                                value smaller than the value passed to this argument will be discarded
-                                (default: 0).
+**Note**
 
-        --t, --translation-table   (Optional) Genetic code to use for CDS translation. Must match the
-                                genetic code used to create the training file (default: 11).
+If the schema was created with chewBBACA&lt;=2.1.0. Please adapt schema with the PrepExternalSchema module to add a config file
 
-        --st, --size-threshold     (Optional) CDS size variation threshold. At the default value of
-                                0.2, alleles with size variation +-20 percent when compared to the
-                                representative will not be included in the final schema (default:
-                                0.2).
-
-        --size-filter              (Optional) Apply the minimum length and size threshold values to
-                                filter out alleles during schema adaptation (default: False).
-    ]]></help>
+    </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From 49804ed0eafe4d5f7973580fab9c8c3f81394530 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 27 Mar 2024 16:39:52 +0100
Subject: [PATCH 32/97] Final AlleleCall.xml with help

---
 tools/chewbbaca/AlleleCall.xml | 93 +++++-----------------------------
 1 file changed, 13 insertions(+), 80 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 933c62b2ea3..ee564c31c80 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -1,4 +1,4 @@
-<tool id="AlleleCall" name="ChewBBACA AlleleCall" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="AlleleCall" name="ChewBBACA AlleleCall" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Determine the allelic profiles of a set of genomes</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
         mkdir './input' &&
         mkdir './schema' &&
         #for $file in $input_file
-        cp $file './input/${file.element_identifier}' &&
+        ln -sf $file './input/${file.element_identifier}' &&
         #end for
         unzip $input_schema -d './schema' &&
         chewBBACA.py AlleleCall
@@ -27,7 +27,7 @@
     ]]></command>
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="true" label="Genome assemblies in FASTA format"/>
-        <param format="zip" name="input_schema" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
             <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
@@ -89,85 +89,18 @@
             </output_collection>
         </test>
     </tests>
-    <help><![CDATA[
-        
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
-==========================
-  chewBBACA - AlleleCall
-==========================
-Performs allele calling to determine the allelic profiles of a set of samples in FASTA format. The
-process identifies new alleles, assigns an integer identifier to those alleles and adds them to the
-schema.
-                                                
-  -i, --input-files [INPUT_FILES]               Path to the directory with the genome FASTA files or
-                                                to a file that contains a list of full paths to the
-                                                FASTA files, one per line. (default: None)
-                                                
-  -g, --schema-directory SCHEMA_DIRECTORY       Path to the schema directory. The schema directory
-                                                contains the loci FASTA files and a folder named
-                                                "short" that contains the FASTA files with the loci
-                                                representative alleles. (default: None)
-                                                
-  -o, --output-directory OUTPUT_DIRECTORY       Output directory where the allele calling results
-                                                will be stored (will create a subdirectory named
-                                                "results_<TIMESTAMP>" if the path passed by the user
-                                                already exists). (default: None)
-                                                
-  --ptf, --training-file PTF_PATH               Path to the Prodigal training file. Default is to
-                                                get the training file from the schema's directory
-                                                (default: None)
-                                                
-  --bsr, --blast-score-ratio BLAST_SCORE_RATIO  BLAST Score Ratio value. Sequences with alignments
-                                                with a BSR value equal to or greater than this value
-                                                will be considered as sequences from the same gene.
-                                                (default: None)
-                                                
-  --l, --minimum-length MINIMUM_LENGTH          Minimum sequence length accepted for a coding
-                                                sequence to be included in the schema. (default:
-                                                None)
-                                                
-  --t, --translation-table TRANSLATION_TABLE    Genetic code used to predict genes and to translate
-                                                coding sequences. Must match the genetic code used
-                                                to create the training file. (default: None)
-                                                
-  --st, --size-threshold SIZE_THRESHOLD         CDS size variation threshold. At the default value
-                                                of 0.2, alleles with size that deviates +-20 percent
-                                                from the locus length mode will be classified as
-                                                ASM/ALM (default: None)
-                                                
-  --pm, --prodigal-mode {single,meta}           Prodigal running mode ("single" for finished
-                                                genomes, reasonable quality draft genomes and big
-                                                viruses. "meta" for metagenomes, low quality draft
-                                                genomes, small viruses, and small plasmids).
-                                                (default: single)
-                                                
-  --no-inferred                                 If provided, the process will not add the sequences
-                                                of inferred alleles (INF) to the schema. Allelic
-                                                profiles will still include the allele identifiers
-                                                attributed to the inferred alleles. Use this
-                                                parameter if the schema is being accessed by
-                                                multiple processes/users simultaneously. (default:
-                                                False)
-                                                
-  --mode {1,2,3,4}                              Execution mode (1: only exact matches at DNA level;
-                                                2: exact matches at DNA and Protein level; 3: exact
-                                                matches and minimizer-based clustering to find
-                                                similar alleles based on BSR+0.1; 4: runs the full
-                                                process to find exact matches and similar matches
-                                                based on BSR value, including the determination of
-                                                new representative alleles to add to the schema).
-                                                (default: 4)
-                                                
+In chewBBACA, by default, an allele needs to be a CDS defined by Prodigal_. To ensure reproducibility of the CDS prediction, the same Prodigal training file for each bacterial species should be used and provided as input.
 
-It is strongly advised to perform allele calling with the default schema parameters to ensure more
-consistent results. Module documentation available at
-https://chewbbaca.readthedocs.io/en/latest/user/modules/AlleleCall.html
+.. class:: infomark
 
-    ]]></help>
+**Important**
+
+Although the use of a training file is optional, it is highly recommended to ensure consistent results.
+
+.. _Prodigal: https://github.com/hyattpd/Prodigal
+    </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From dec0a573fcb0d94e2fe02c44d9a6f2803304b488 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 28 Mar 2024 15:49:56 +0100
Subject: [PATCH 33/97] NSStats.xml reviewed

---
 tools/chewbbaca/NSStats.xml | 36 ++++++++++--------------------------
 1 file changed, 10 insertions(+), 26 deletions(-)

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index cb573d72e11..07cfe4af552 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -7,40 +7,24 @@
     <command detect_errors="exit_code"><![CDATA[
         chewBBACA.py NSStats
             -m $mode
+            #if $species_id != ""
             --sp $species_id 
+            #end if
+            #if $schema_id != ""
             --sc $schema_id
-            --ns $nomenclature_server > NSStats.txt
+            #end if
+            > NSStats.txt
     ]]></command>
     <inputs>
         <param argument="--mode" type="select" label="Mode" optional="false">
-            <option value="species">species: </option>
-            <option value="schemas">schemas: </option>
+            <option value="species">species</option>
+            <option value="schemas">schemas</option>
         </param>
-        <param argument="--species-id" type="select" label="Species ID" optional="true">
-            <option value="1">Streptococcus pyogenes</option>
-            <option value="2">Acinetobacter baumannii</option>
-            <option value="3">Arcobacter butzleri</option>
-            <option value="4">Campylobacter jejuni</option>
-            <option value="5">Escherichia coli</option>
-            <option value="6">Listeria monocytogenes</option>
-            <option value="7">Yersinia enterocolitica</option>
-            <option value="8">Salmonella enterica</option>
-            <option value="9">Streptococcus agalactiae</option>
-            <option value="10">Brucella melitensis</option>
-            <option value="11">Brucella</option>
-            <option value="12">Clostridium perfringens</option>
-            <option value="13">Clostridium chauvoei</option>
-            <option value="14">Bacillus anthracis</option>
-            <option value="15">Klebsiella oxytoca</option>
-            <option value="16">Clostridium neonatale</option>
+        <param argument="--species-id" type="select" label="Species ID" value="" optional="true">
+            <expand macro="species_id"/>
         </param>
         <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
-        <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID" optional="true"/>
-        <param argument="--nomenclature-server" type="select" label="Nomenclature server" optional="false">
-            <option value="main" selected="true">main "https://chewbbaca.online/"</option>
-            <option value="tutorial">tutorial "https://tutorial.chewbbaca.online/"</option>
-            <option value="local">local "http://127.0.0.1:5000/NS/api/"</option>                
-        </param>
+        <param argument="--schema-id" type="integer" min="1" value="" label="Schema ID" optional="true"/>
     </inputs>
     <outputs>
         <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name}"/>

From fcfc8065d5378e0a7dca2de88f955790286fc396 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 28 Mar 2024 15:50:30 +0100
Subject: [PATCH 34/97] macros updated species_id

---
 tools/chewbbaca/macros.xml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/tools/chewbbaca/macros.xml b/tools/chewbbaca/macros.xml
index ab844c88bb1..2958f5557e7 100644
--- a/tools/chewbbaca/macros.xml
+++ b/tools/chewbbaca/macros.xml
@@ -16,4 +16,22 @@
             <citation type="doi">10.1099/mgen.0.000166</citation>
         </citations>
     </xml>
+    <xml name="species_id">
+        <option value="1">Streptococcus pyogenes</option>
+        <option value="2">Acinetobacter baumannii</option>
+        <option value="3">Arcobacter butzleri</option>
+        <option value="4">Campylobacter jejuni</option>
+        <option value="5">Escherichia coli</option>
+        <option value="6">Listeria monocytogenes</option>
+        <option value="7">Yersinia enterocolitica</option>
+        <option value="8">Salmonella enterica</option>
+        <option value="9">Streptococcus agalactiae</option>
+        <option value="10">Brucella melitensis</option>
+        <option value="11">Brucella</option>
+        <option value="12">Clostridium perfringens</option>
+        <option value="13">Clostridium chauvoei</option>
+        <option value="14">Bacillus anthracis</option>
+        <option value="15">Klebsiella oxytoca</option>
+        <option value="16">Clostridium neonatale</option>
+    </xml>
 </macros>

From e5ed80e79d2b0ae6a22a3e5980299f84154ed9f4 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 10:59:40 +0200
Subject: [PATCH 35/97] revised CreateSchenma

---
 tools/chewbbaca/CreateSchema.xml | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index ad6b0304644..7454748f910 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -13,10 +13,7 @@
             #if str($training_file) != 'None'
                 --ptf '$training_file'
             #end if
-            --bsr $blast_score_ratio
-            --l $minimum_length
-            --t $translation_table
-            --st $size_threshold
+            @INPUT@
             --pm $prodigal_mode
             -i './input' -o './output' &&
         cd output/ &&
@@ -26,11 +23,9 @@
         <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--blast_score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
             <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
-            <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
-            <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
-            <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">
+            <expand macro="param" />
+            <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="&quot;single&quot; for finished genomes, reasonable quality draft genomes and big viruses. &quot;meta&quot; for metagenomes, low quality draft genomes, small viruses, and small plasmids">
                 <option value="single" selected="true">
                         single
                     </option>
@@ -60,6 +55,7 @@
         </test>
     </tests>
     <help>
+        
 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
 A Schema is a pre-defined set of loci that is used in MLST analyses. Traditional MLST schemas relied in 7 loci that were internal fragments of housekeeping genes and each locus was defined by its amplification by a pair of primers yielding a fragment of a defined size.

From d2fab387b2fb0ec16b3bd2995eec5b9c281456f9 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 11:04:06 +0200
Subject: [PATCH 36/97] revised CreateSchema with another test

---
 tools/chewbbaca/CreateSchema.xml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 7454748f910..79598658111 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -53,6 +53,11 @@
         <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
         <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip" compare="sim_size"/>
         </test>
+        <test>
+            <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
+            <param name="training_file" value="Streptococcus_agalactiae.trn"/>
+            <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed_trn.zip" compare="sim_size"/>
+        </test>
     </tests>
     <help>
         

From 4a280bac6ff4b5b260b9da5dbd0dab4af57883a9 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 11:45:57 +0200
Subject: [PATCH 37/97] revised AlleleCall.xml

---
 tools/chewbbaca/AlleleCall.xml | 67 +++++++++++++++++++++++++++++-----
 1 file changed, 57 insertions(+), 10 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index ee564c31c80..c7adc57ba8f 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -14,28 +14,49 @@
         chewBBACA.py AlleleCall
             #if str($training_file) != 'None'
                 --ptf $training_file
-            #end if            
-            --bsr $blast_score_ratio
+            #end if
+            #if str($genes_list) != 'None'
+                --gl $genes_list
+            #end if
+            #if str($blast_score_ratio) != ""
+                --bsr $blast_score_ratio
+            #end if
+            #if str($minimum_length) != ""
             --l $minimum_length
+            #end if
+            #if str($translation_table) != ""
             --t $translation_table
+            #end if
+            #if str($size_threshold) != ""
             --st $size_threshold
+            #end if
             $no_inferred
             --pm $prodigal_mode
             --mode $mode
             --force-continue
+            #if 'output_unclassified' in $output_selector:
+                --output-unclassified
+            #end if
+            #if 'output_missing' in $output_selector:
+                --output-missing
+            #end if
+            #if 'output_novel' in $output_selector:
+                --output-novel
+            #end if
             -i './input' -g './schema/schema_seed/' -o './output'
     ]]></command>
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="true" label="Genome assemblies in FASTA format"/>
         <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
+            <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
-            <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
-            <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
-            <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
-            <param argument="--no-inferred" type="boolean" truevalue="--no-inferred" falsevalue="" checked="false" label="Add the sequences of inferred alleles (INF) to the schema" help="Use this parameter if the schema is being accessed by multiple processes/users simultaneously." />
-            <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="single for finished genomes, reasonable quality draft genomes and big viruses. meta for metagenomes, low quality draft genomes, small viruses, and small plasmids">
+            <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="" optional="true" label="BLAST Score Ratio value" /> 
+            <param argument="--minimum-length" type="integer" min="0" value="" optional="true" label="Minimum sequence length value"/>
+            <param argument="--translation-table" type="integer" min="0" value="" optional="true" label="Genetic code used to predict genes and to translate coding sequences"/>
+            <param argument="--size-threshold" type="float" min="0" value="" optional="true" label="CDS size variation threshold"/>
+            <param argument="--no-inferred" type="boolean" truevalue="--no-inferred" falsevalue="" checked="false" optional="true" label="Add the sequences of inferred alleles (INF) to the schema" help="Use this parameter if the schema is being accessed by multiple processes/users simultaneously." />
+            <param argument="--prodigal-mode" type="select" optional="true" label="Prodigal Mode" help="&quot;single&quot; for finished genomes, reasonable quality draft genomes and big viruses. &quot;meta&quot; for metagenomes, low quality draft genomes, small viruses, and small plasmids">
                 <option value="single" selected="true">
                         single
                     </option>
@@ -43,13 +64,20 @@
                         meta
                     </option>
             </param>
-            <param argument="--mode" type="select" label="Execution mode" >
+            <param argument="--mode" type="select" label="Execution mode" optional="true">
                 <option value="1">Only exact matches at DNA level</option>
                 <option value="2">Exact matches at DNA and Protein level </option>
                 <option value="3">Exact matches and minimizer-based clustering to find similar alleles based on BSR+0.1 </option>
                 <option value="4" selected="true">Exact matches and minimizer-based clustering to find similar alleles based on BSR+0.1 </option>
             </param>
         </section>
+        <section name="output" title="Output Options">
+            <param name="output_selector" type="select" multiple="true" optional="true" display="checkboxes" label="Select / Deselect all">
+                <option value="output_unclassified">Create a Fasta file with unclassified coding sequences</option>
+                <option value="output_missing">Create a Fasta file with coding sequences classified as NIPH, NIPHEM, ASM, ALM, PLOT3, PLOT5 and LOTSC</option>
+                <option value="output_novel ">Create Fasta file with the novel alleles inferred during the allele calling</option>
+            </param>
+        </section>
     </inputs>
     <outputs>
         <collection name="allelecall_results" type="list" label="${tool.name} on ${on_string}: AlleleCall Results">
@@ -58,9 +86,18 @@
         <collection name="allelcall_log" type="list" label="${tool.name} on ${on_string}: AlleleCall Logs">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" format="txt" directory="./output"/>
         </collection>
+        <data name="unclassified_fasta" format="fasta" from_work_dir="./output" label="${tool.name} on ${on_string}: Unclassified fasta">
+            <filter>output_selector['output_unclassified']</filter>
+        </data>
+        <data name="missing_fasta" format="fasta" from_work_dir="./output" label="${tool.name} on ${on_string}: Missing fasta">
+            <filter>output_selector['output_missing']</filter>
+        </data>
+        <data name="novel_fasta" format="fasta" from_work_dir="./output" label="${tool.name} on ${on_string}: Novel fasta">
+            <filter>output_selector['output_novel']</filter>
+        </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="5">
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
             <output_collection name="allelecall_results" type="list">
@@ -100,6 +137,16 @@ In chewBBACA, by default, an allele needs to be a CDS defined by Prodigal_. To e
 
 Although the use of a training file is optional, it is highly recommended to ensure consistent results.
 
+If the schema files are created by chewBBACA v2, please use the PrepExternalSchema module to convert the schema to a format fully compatible with chewBBACA v3.
+
+By default, the AlleleCall module uses the Prodigal training file included in the schema’s directory and it is not necessary to pass a training file to the --ptf parameter.
+
+.. class:: infomark
+
+**Note**
+
+If a text file that contains a list of full paths to loci FASTA files or loci IDs, one per line, is passed to the --genes-list parameter, the process will only perform allele calling for the loci in that list.
+
 .. _Prodigal: https://github.com/hyattpd/Prodigal
     </help>
     <expand macro="citations" />

From c871034c93add574e14d370013b2a1091510f0f0 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 12:14:35 +0200
Subject: [PATCH 38/97] revised AlleleCallEvaluator.xml

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 70 +++++++++++--------------
 1 file changed, 32 insertions(+), 38 deletions(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index fb012e5f032..bfe4dd27978 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -1,4 +1,4 @@
-<tool id="AlleleCallEvaluator" name="chewBBACA AlleleCallEvaluator" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="AlleleCallEvaluator" name="chewBBACA AlleleCallEvaluator" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Build an interactive report for allele calling results evaluation</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
         mkdir './input' &&
         mkdir './schema' &&
         #for $file in $input_file
-        cp $file './input/${file.element_identifier}' &&
+        ln -sf $file './input/${file.element_identifier}' &&
         #end for
         unzip $input_schema -d './schema' &&
         chewBBACA.py AlleleCallEvaluator
@@ -25,10 +25,10 @@
     ]]></command>
     <inputs>
         <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
-        <param name="input_schema" format="zip" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <param name="input_schema" format="zip" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
             <param argument="--annotations" type="data" format="tabular" label="Annotation file" help="File created by the UniprotFinder module" optional="true" />
-            <param argument="--light" type="boolean" truevalue="--light" falsevalue="" checked="false" label="Do not compute the presence-absence matrix, the distance matrix  and the Neighbor-Joining tree." />
+            <param argument="--light" type="boolean" truevalue="--light" falsevalue="" checked="false" label="Do not compute the presence-absence matrix, the distance matrix,  and the Neighbor-Joining tree." />
             <param argument="--no-pa" type="boolean" truevalue="--no-pa " falsevalue="" checked="false" label="Do not compute the presence-absence matrix" />
             <param argument="--no-dm" type="boolean" truevalue="--no-dm " falsevalue="" checked="false" label="Do not compute the distance matrix" />
             <param argument="--no-tree" type="boolean" truevalue="--no-tree " falsevalue="" checked="false" label="Do not compute the Neighbor-Joining tree" />
@@ -51,43 +51,37 @@
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
             <output name="allelecall_report" file="allelecall_report.html" compare="sim_size"/>
         </test>
+        <test>
+            <param name="input_file">
+                <collection type="list">
+                    <element name="cds_coordinates.tsv" value="cds_coordinates.tsv" ftype="tabular"/>
+                    <element name="loci_summary_stats.tsv" value="loci_summary_stats.tsv" ftype="tabular"/>
+                    <element name="results_alleles.tsv" value="results_alleles.tsv" ftype="tabular"/>
+                    <element name="results_statistics.tsv" value="results_statistics.tsv" ftype="tabular"/>
+                </collection>
+            </param>
+            <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <param name="annotations" value="schema_seed_annotations.tsv"/>
+            <output name="allelecall_report" file="allelecall_report_annot.html" compare="sim_size"/>
+        </test>
     </tests>
-    <help><![CDATA[
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
+
+The AlleleCallEvaluator module allows users to generate an interactive HTML report to evaluate allele calling results generated by the AlleleCall module. The report provides summary statistics to evaluate results per sample and per locus (with the possibility to provide a TSV file with loci annotations to include on a table). The report includes components to display a heatmap representing the loci presence-absence matrix, a heatmap representing the distance matrix based on allelic differences and a Neighbor-Joining (NJ) tree based on the MSA of the core genome loci.
+
+.. class:: infomark
+
+**Note**
+
+You have to uncompress the archive and open the HTML file with a browser.
+
+.. class:: warningmark
 
-===================================
-  chewBBACA - AlleleCallEvaluator
-===================================
+**Warning**
 
-  -i, --input-files INPUT_FILES            Path to the directory that contains the allele calling
-                                           results. (default: None)
-                                           
-  -g, --schema-directory SCHEMA_DIRECTORY  Path to the schema directory. (default: None)
-                                           
-  -o, --output-directory OUTPUT_DIRECTORY  Path to the output directory where the report HTML files
-                                           will be generated. (default: None)
-                                           
-  -a, --annotations ANNOTATIONS            Path to the TSV file created by the UniprotFinder module.
-                                           (default: None)
-                                           
-  --light                                  Do not compute the presence-absence matrix, the distance
-                                           matrix and the Neighbor-Joining tree. (default: False)
-                                           
-  --no-pa                                  Do not compute the presence-absence matrix. (default:
-                                           False)
-                                           
-  --no-dm                                  Do not compute the distance matrix. (default: False)
-                                           
-  --no-tree                                Do not compute the Neighbor-Joining tree. (default:
-                                           False)
-                                           
-  --cg-alignment                           Compute the MSA of the core genome loci, even if --no-
-                                           tree is provided. (default: False)
+The JS bundle is necessary to visualize the HTML report. Do not move or delete this file.
 
-    ]]></help>
+    </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From 85b2a0d486c040b054432bfc0a741ac457b0d5ee Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 13:08:32 +0200
Subject: [PATCH 39/97] revised DownloadSchema

---
 tools/chewbbaca/DownloadSchema.xml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
index b6b3fb22ad7..4f7e1328303 100644
--- a/tools/chewbbaca/DownloadSchema.xml
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -34,11 +34,6 @@
         </param>
         <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
         <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>
-        <param argument="--nomenclature-server" type="select" label="Nomenclature server" optional="false">
-            <option value="main" selected="true">main "https://chewbbaca.online/"</option>
-            <option value="tutorial">tutorial "https://tutorial.chewbbaca.online/"</option>
-            <option value="local">local "http://127.0.0.1:5000/NS/api/"</option>                
-        </param>
     </inputs>
     <outputs>
         <data format="zip" name="schema" from_work_dir="schema_seed.zip" label="${tool.name} Schema files"/>
@@ -51,6 +46,7 @@
         </test>
     </tests>
     <help>
+        
 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
 The DownloadSchema module enables the download of schemas from the Chewie-NS server.

From cdfd1215f58d62141b0242db4b6a11673b6cd571 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 13:39:07 +0200
Subject: [PATCH 40/97] revised ExtractCgMLST.xml

---
 tools/chewbbaca/ExtractCgMLST.xml | 37 ++++++++++---------------------
 1 file changed, 12 insertions(+), 25 deletions(-)

diff --git a/tools/chewbbaca/ExtractCgMLST.xml b/tools/chewbbaca/ExtractCgMLST.xml
index c20f609c4ff..57c0403a8e2 100644
--- a/tools/chewbbaca/ExtractCgMLST.xml
+++ b/tools/chewbbaca/ExtractCgMLST.xml
@@ -1,4 +1,4 @@
-<tool id="ExtractCgMLST" name="chewBBACA ExtractCgMLST" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="ExtractCgMLST" name="chewBBACA ExtractCgMLST" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Determine the set of loci that constitute the core genome</description>
     <macros>
         <import>macros.xml</import>
@@ -7,7 +7,7 @@
     <command detect_errors="exit_code"><![CDATA[
         mkdir './input' &&
         #for $file in $input_file
-        cp $file './input/${file.element_identifier}' &&
+        ln -sf $file './input/${file.element_identifier}.tsv' &&
         #end for
         chewBBACA.py ExtractCgMLST
         --t $threshold
@@ -27,7 +27,7 @@
             <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values">
                 <validator type="regex">[ .0-9]+</validator>
             </param>
-            <param name="genes2remove" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove paralogous counts?" help="--genes2remove"/>
+            <param name="genes2remove" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove paralogous counts?" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process. --genes2remove"/>
         </section>
     </inputs>
     <outputs>
@@ -37,35 +37,22 @@
         <test>
             <param name="input_file">
                 <collection type="list">
-                    <element name="results_alleles.tsv" value="results_alleles.tsv" ftype="tabular"/>
+                    <element name="results_alleles" value="results_alleles.tsv" ftype="tabular"/>
                 </collection>
             </param>
             <output name="ExtractCgMLST" file="ExtractCgMLST.zip" compare="sim_size"/>
         </test>
     </tests>
-    <help><![CDATA[
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
-=============================
-  chewBBACA - ExtractCgMLST
-=============================
-  --t, --threshold THRESHOLD [THRESHOLD ...]  Genes that constitute the core genome must be in a
-                                              proportion of genomes that is at least equal to this
-                                              value. Users can provide multiple values. (default:
-                                              [0.95, 0.99, 1])
+cgMLST schemas are defined as the set of loci that are present in all strains under analysis or, due to sequencing/assembly limitations, >95% of strains analyzed. In order to have a robust definition of a cgMLST schema for a given bacterial species, a set of representative strains of the diversity of a given species should be selected. 
 
-  --r, --genes2remove GENES2REMOVE            Path to file with a list of genes/columns to remove
-                                              from the matrix (one gene identifier per line).
-                                              (default: False)
-                                              
-  --g, --genomes2remove GENOMES2REMOVE        Path to file with a list of genomes/rows to remove
-                                              from the matrix (one genome identifier per line).
-                                              (default: False)
+.. class:: infomark
 
-    ]]></help>
+**Note**
+
+The user can define a **space-separated** list of values for --threshold
+    </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From 91a8efbe5affe005de02c9b9a6f4d4be3853791c Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 13:39:45 +0200
Subject: [PATCH 41/97] updated macros - INPUT as token

---
 tools/chewbbaca/macros.xml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tools/chewbbaca/macros.xml b/tools/chewbbaca/macros.xml
index 2958f5557e7..c4dd07ad70f 100644
--- a/tools/chewbbaca/macros.xml
+++ b/tools/chewbbaca/macros.xml
@@ -34,4 +34,15 @@
         <option value="15">Klebsiella oxytoca</option>
         <option value="16">Clostridium neonatale</option>
     </xml>
+    <token name="@INPUT@">
+        --bsr $blast_score_ratio
+        --l $minimum_length
+        --t $translation_table
+        --st $size_threshold
+    </token>
+    <xml name="param">
+        <param argument="--blast_score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
+        <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
+        <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+    </xml>
 </macros>

From 56a4bcb588dcf273e9f28dbf6e79686d3782ff03 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 13:43:20 +0200
Subject: [PATCH 42/97] Revised PrepExternalSchema.xml

---
 tools/chewbbaca/PrepExternalSchema.xml | 16 +++-------------
 1 file changed, 3 insertions(+), 13 deletions(-)

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index 18a7193a2f4..f846e56dfd7 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -11,10 +11,7 @@
             #if str($training_file) != 'None'
                 --ptf '$training_file'
             #end if            
-            --bsr $blast_score_ratio
-            --l $minimum_length
-            --t $translation_table
-            --st $size_threshold
+            @INPUT@
             $size_filter
             -g './schema/schema_seed/' -o './schema_seed' &&
         zip -r PExternalschema_seed.zip './schema_seed'
@@ -23,10 +20,8 @@
         <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
             <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
-            <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
-            <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+            <expand macro="param" />
             <param argument="--size-filter" type="boolean" truevalue="--size-filter" falsevalue="" checked="false" label="Size filter" help="Apply the minimum length and size threshold values to filter out alleles during schema adaptation" />
         </section>
     </inputs>
@@ -41,16 +36,11 @@
         </test>
     </tests>
     <help>
+        
 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
 The PrepExternalSchema module enables the adaptation of external schemas so that it is possible to use those schemas with chewBBACA.
 
-.. class:: infomark
-
-**Note**
-
-If the schema was created with chewBBACA&lt;=2.1.0. Please adapt schema with the PrepExternalSchema module to add a config file
-
     </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From 44e833116068df645258fcee287b7444e12498ff Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 16:03:07 +0200
Subject: [PATCH 43/97] revised Joinprofile.xml

---
 tools/chewbbaca/JoinProfiles.xml | 37 +++++++++++++-------------------
 1 file changed, 15 insertions(+), 22 deletions(-)

diff --git a/tools/chewbbaca/JoinProfiles.xml b/tools/chewbbaca/JoinProfiles.xml
index c6f7413eec2..a287bff97e5 100644
--- a/tools/chewbbaca/JoinProfiles.xml
+++ b/tools/chewbbaca/JoinProfiles.xml
@@ -1,43 +1,36 @@
-<tool id="JoinProfiles" name="chewBBACA JoinProfiles" version="@CHEW_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="JoinProfiles" name="chewBBACA JoinProfiles" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Join allele calling results from different runs</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[      
+    <command detect_errors="exit_code"><![CDATA[
+        #set $profiles = $input1
+        #set $profile_tmp = []
+        #for $i, $k in enumerate($profiles)
+            ln -s '$k' './profile_${i}.tsv' &&
+            $profile_tmp.append("profile_" + str($i) + ".tsv")
+        #end for
         chewBBACA.py JoinProfiles
-            -p $input1
-            #for $q in $queries 
-                '${q.input2}'
-            #end for
+            -p ${' '.join($profile_tmp)}
             -o JoinedProfile.tsv
     ]]></command>
     <inputs>
-        <param name="input1" type="data" format="tsv" multiple="false" label="AlleleCall results" />
-        <repeat name="queries" title="AlleleCall results to join">
-            <param name="input2" type="data" format="tsv" label="Select"/>
-        </repeat>
+        <param name="input1" type="data" format="tsv" multiple="true" label="AlleleCall results" />
     </inputs>
     <outputs>
         <data format="tsv" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>
     </outputs>
     <tests>
         <test>
-            <param name="input1" value="results_alleles.tsv"/>
-            <param name="input2" value="results_alleles.tsv"/>
+            <param name="input1" value="results_alleles.tsv,results_alleles2.tsv"/>
             <output name="JoinedProfile" file="JoinedProfile.tsv" compare="sim_size"/>
         </test>
     </tests>
-    <help><![CDATA[
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
-============================
-  chewBBACA - JoinProfiles
-============================
-    ]]></help>
+The process creates a TSV file with the allelic profiles of all samples in the input files.
+    </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From 5c66c2c05728738a9858e552aee9b675d3a103b8 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 16:14:45 +0200
Subject: [PATCH 44/97] Added --cds_input

---
 tools/chewbbaca/CreateSchema.xml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 79598658111..100fa6f4a43 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -13,6 +13,9 @@
             #if str($training_file) != 'None'
                 --ptf '$training_file'
             #end if
+            #if str($cds_input) != 'None'
+                --cds '$cds_input'
+            #end if
             @INPUT@
             --pm $prodigal_mode
             -i './input' -o './output' &&
@@ -23,6 +26,7 @@
         <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--cds_input" type="data" format="txt" label="CDS input" optional="true" />
             <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
             <expand macro="param" />
             <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="&quot;single&quot; for finished genomes, reasonable quality draft genomes and big viruses. &quot;meta&quot; for metagenomes, low quality draft genomes, small viruses, and small plasmids">
@@ -53,7 +57,7 @@
         <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
         <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip" compare="sim_size"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
             <param name="training_file" value="Streptococcus_agalactiae.trn"/>
             <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed_trn.zip" compare="sim_size"/>
@@ -83,6 +87,12 @@ These definitions are always operational in nature, in the sense that the analys
 
 The use of a prodigal training file for schema creation is highly recommended.
 
+.. class:: infomark
+
+**Important**
+
+If you provide the --cds-input parameter, chewBBACA assumes that the input FASTA files contain coding sequences and skips the gene prediction step with Prodigal. To avoid issues related with the format of the sequence headers, chewBBACA renames the sequence headers based on the unique basename prefix determined for each input file and on the order of the coding sequences (e.g.: coding sequences inside a file named GCF_000007125.1_ASM712v1_cds_from_genomic.fna are renamed to GCF_000007125-protein1, GCF_000007125-protein2, …, GCF_000007125-proteinN).
+
     </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From 08efc33a7a95b549d05e7d2fd8a6eef10374a37d Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 16:15:45 +0200
Subject: [PATCH 45/97] Added --cds_input

---
 tools/chewbbaca/CreateSchema.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 100fa6f4a43..a943c2086b3 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -91,7 +91,7 @@ The use of a prodigal training file for schema creation is highly recommended.
 
 **Important**
 
-If you provide the --cds-input parameter, chewBBACA assumes that the input FASTA files contain coding sequences and skips the gene prediction step with Prodigal. To avoid issues related with the format of the sequence headers, chewBBACA renames the sequence headers based on the unique basename prefix determined for each input file and on the order of the coding sequences (e.g.: coding sequences inside a file named GCF_000007125.1_ASM712v1_cds_from_genomic.fna are renamed to GCF_000007125-protein1, GCF_000007125-protein2, …, GCF_000007125-proteinN).
+If you provide the **--cds-input** parameter, chewBBACA assumes that the input FASTA files contain coding sequences and skips the gene prediction step with Prodigal. To avoid issues related with the format of the sequence headers, chewBBACA renames the sequence headers based on the unique basename prefix determined for each input file and on the order of the coding sequences (e.g.: coding sequences inside a file named GCF_000007125.1_ASM712v1_cds_from_genomic.fna are renamed to GCF_000007125-protein1, GCF_000007125-protein2, …, GCF_000007125-proteinN).
 
     </help>
     <expand macro="citations" />

From a7a4520d52050547bf04ac5268e75a815d57397e Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 16:28:39 +0200
Subject: [PATCH 46/97] Added --cds-input

---
 tools/chewbbaca/AlleleCall.xml   | 14 +++++++++++---
 tools/chewbbaca/CreateSchema.xml |  2 +-
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index c7adc57ba8f..11158671d26 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -15,6 +15,9 @@
             #if str($training_file) != 'None'
                 --ptf $training_file
             #end if
+            #if str($cds_input) != 'None'
+                --cds '$cds_input'
+            #end if
             #if str($genes_list) != 'None'
                 --gl $genes_list
             #end if
@@ -43,6 +46,9 @@
             #if 'output_novel' in $output_selector:
                 --output-novel
             #end if
+            #if 'hash_profile' in $output_selector:
+                --hash-profile 
+            #end if
             -i './input' -g './schema/schema_seed/' -o './output'
     ]]></command>
     <inputs>
@@ -51,6 +57,7 @@
         <section name="advanced" title="Advanced options">
             <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--cds_input" type="data" format="txt" label="CDS input" optional="true" />
             <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="" optional="true" label="BLAST Score Ratio value" /> 
             <param argument="--minimum-length" type="integer" min="0" value="" optional="true" label="Minimum sequence length value"/>
             <param argument="--translation-table" type="integer" min="0" value="" optional="true" label="Genetic code used to predict genes and to translate coding sequences"/>
@@ -73,9 +80,10 @@
         </section>
         <section name="output" title="Output Options">
             <param name="output_selector" type="select" multiple="true" optional="true" display="checkboxes" label="Select / Deselect all">
-                <option value="output_unclassified">Create a Fasta file with unclassified coding sequences</option>
-                <option value="output_missing">Create a Fasta file with coding sequences classified as NIPH, NIPHEM, ASM, ALM, PLOT3, PLOT5 and LOTSC</option>
-                <option value="output_novel ">Create Fasta file with the novel alleles inferred during the allele calling</option>
+                <option value="output_unclassified">Create a Fasta file with unclassified coding sequences. (--output-unclassified)</option>
+                <option value="output_missing">Create a Fasta file with coding sequences classified as NIPH, NIPHEM, ASM, ALM, PLOT3, PLOT5 and LOTSC. (--output-missing)</option>
+                <option value="output_novel ">Create Fasta file with the novel alleles inferred during the allele calling. (--output-novel)</option>
+                <option value="hash_profile ">Create TSV file with hashed allelic profiles. (--hash-profile) </option>
             </param>
         </section>
     </inputs>
diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index a943c2086b3..703d09f7629 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -26,7 +26,7 @@
         <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--cds_input" type="data" format="txt" label="CDS input" optional="true" />
+            <param argument="--cds-input" type="data" format="txt" label="CDS input" optional="true" />
             <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
             <expand macro="param" />
             <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="&quot;single&quot; for finished genomes, reasonable quality draft genomes and big viruses. &quot;meta&quot; for metagenomes, low quality draft genomes, small viruses, and small plasmids">

From ca1f086a19e279594e2af87b007a30e7736d3c84 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 16:29:05 +0200
Subject: [PATCH 47/97] Added --cds-input

---
 tools/chewbbaca/AlleleCall.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 11158671d26..1fdb75b1549 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -57,7 +57,7 @@
         <section name="advanced" title="Advanced options">
             <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--cds_input" type="data" format="txt" label="CDS input" optional="true" />
+            <param argument="--cds-input" type="data" format="txt" label="CDS input" optional="true" />
             <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="" optional="true" label="BLAST Score Ratio value" /> 
             <param argument="--minimum-length" type="integer" min="0" value="" optional="true" label="Minimum sequence length value"/>
             <param argument="--translation-table" type="integer" min="0" value="" optional="true" label="Genetic code used to predict genes and to translate coding sequences"/>

From 5b4a0b7cdb43bbbc01a92fd481219ccdbc6044a3 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 16:33:03 +0200
Subject: [PATCH 48/97] Added --genes-list

---
 tools/chewbbaca/PrepExternalSchema.xml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index f846e56dfd7..fe9f919ee2c 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -10,7 +10,10 @@
         chewBBACA.py PrepExternalSchema
             #if str($training_file) != 'None'
                 --ptf '$training_file'
-            #end if            
+            #end if
+            #if str($genes_list) != 'None'
+                --gl $genes_list
+            #end if    
             @INPUT@
             $size_filter
             -g './schema/schema_seed/' -o './schema_seed' &&
@@ -20,6 +23,7 @@
         <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
             <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
             <expand macro="param" />
             <param argument="--size-filter" type="boolean" truevalue="--size-filter" falsevalue="" checked="false" label="Size filter" help="Apply the minimum length and size threshold values to filter out alleles during schema adaptation" />

From f39fec1176ef36a96ee06bd8bb9609e2caaf1593 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 16:46:14 +0200
Subject: [PATCH 49/97] added --common

---
 tools/chewbbaca/JoinProfiles.xml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/tools/chewbbaca/JoinProfiles.xml b/tools/chewbbaca/JoinProfiles.xml
index a287bff97e5..9780fdee590 100644
--- a/tools/chewbbaca/JoinProfiles.xml
+++ b/tools/chewbbaca/JoinProfiles.xml
@@ -14,9 +14,11 @@
         chewBBACA.py JoinProfiles
             -p ${' '.join($profile_tmp)}
             -o JoinedProfile.tsv
+            $common
     ]]></command>
     <inputs>
         <param name="input1" type="data" format="tsv" multiple="true" label="AlleleCall results" />
+        <param argument="--common" type="boolean" truevalue="--common" falsevalue="" checked="false" label="Common" optional="true" help="Create file with profiles for the set of common loci" />
     </inputs>
     <outputs>
         <data format="tsv" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>
@@ -31,6 +33,12 @@
 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
 
 The process creates a TSV file with the allelic profiles of all samples in the input files.
+
+.. class:: infomark
+
+**Important**
+
+It is necessary to pass the --common argument if the input files do not have the same set of loci (this option creates a new file only with the set of loci shared between all input files).
     </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file

From dd62428757220ce6ec1493193611f05d8f9baa28 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 2 Apr 2024 16:48:54 +0200
Subject: [PATCH 50/97] update test-data

---
 ...007265.1_ASM726v1_PExternalschema_seed.zip | Bin 115704 -> 115704 bytes
 .../GCA_000007265.1_ASM726v1_schema_seed.zip  | Bin 115704 -> 115704 bytes
 tools/chewbbaca/test-data/NSStats.txt         |  39 -------
 .../test-data/Streptococcus_agalactiae.trn    | Bin 0 -> 558392 bytes
 .../test-data/allelecall_report.html          |   2 +-
 .../test-data/allelecall_report_annot.html    |  16 +++
 .../chewbbaca/test-data/results_alleles2.tsv  |   2 +
 .../test-data/results_statistics.tsv          |   2 +-
 .../test-data/schema_seed_annotations.tsv     | 103 ++++++++++++++++++
 9 files changed, 123 insertions(+), 41 deletions(-)
 create mode 100644 tools/chewbbaca/test-data/Streptococcus_agalactiae.trn
 create mode 100644 tools/chewbbaca/test-data/allelecall_report_annot.html
 create mode 100644 tools/chewbbaca/test-data/results_alleles2.tsv
 create mode 100644 tools/chewbbaca/test-data/schema_seed_annotations.tsv

diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip
index dcee05e373222b00502dccbd34deef6a9b8014fb..5106c0d45882189858b6f782783b6bfa04b82ffb 100644
GIT binary patch
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diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
index e49bf9d3022d5ac9174112a1f0b3ad2f18ee39f5..ffd5a982bd4943cc503a9e71666e99eea923b19b 100644
GIT binary patch
delta 9195
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delta 9195
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diff --git a/tools/chewbbaca/test-data/NSStats.txt b/tools/chewbbaca/test-data/NSStats.txt
index 8372b0424fa..e69de29bb2d 100644
--- a/tools/chewbbaca/test-data/NSStats.txt
+++ b/tools/chewbbaca/test-data/NSStats.txt
@@ -1,39 +0,0 @@
-
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
-
-=======================
-  chewBBACA - NSStats
-=======================
-Started at: 2024-03-27T13:51:03
-
-
-Retrieving data...
-
-------------------------------------------------------------------------------
-Species                             id       #schemas     #loci      #alleles 
-------------------------------------------------------------------------------
-Streptococcus pyogenes              1           1          3044       398511  
-Acinetobacter baumannii             2           1          2390       701606  
-Arcobacter butzleri                 3           1          7474       82419   
-Campylobacter jejuni                4           1          2794       299214  
-Escherichia coli                    5           1          7601      2963736  
-Listeria monocytogenes              6           1          1748       371020  
-Yersinia enterocolitica             7           1          6344       154555  
-Salmonella enterica                 8           1          8558      2879459  
-Streptococcus agalactiae            9           1          3641       248987  
-Brucella melitensis                 10          1          2762       11222   
-Brucella                            11          1          1764       78557   
-Clostridium perfringens             12          1          1431       152324  
-Clostridium chauvoei                13          1          2223        7711   
-Bacillus anthracis                  14          1          3803       52474   
-Klebsiella oxytoca                  15          1          4201       132939  
-Clostridium neonatale               16          1          2350       13115   
-------------------------------------------------------------------------------
-
-
-Finished at: 2024-03-27T13:51:07
-Took  0m 4s.
diff --git a/tools/chewbbaca/test-data/Streptococcus_agalactiae.trn b/tools/chewbbaca/test-data/Streptococcus_agalactiae.trn
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diff --git a/tools/chewbbaca/test-data/allelecall_report.html b/tools/chewbbaca/test-data/allelecall_report.html
index 6e7b82c45e2..423fe059c6e 100644
--- a/tools/chewbbaca/test-data/allelecall_report.html
+++ b/tools/chewbbaca/test-data/allelecall_report.html
@@ -9,7 +9,7 @@
 <body style="background-color: #f6f6f6">
     <noscript> You need to enable JavaScript to run this app. </noscript>
     <div id="root"></div>
-    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"], "loci_data": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 10, 104, 114]]}], "loci_stats": [{"columns": ["Locus", "Total CDSs", "Valid Classes", "Invalid Classes", "Proportion Samples", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [["GCA-000007265-protein1", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein58", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein67", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein66", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein65", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein64", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein63", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein62", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein61", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein60", 1, 1, 0, 1.0, 1, 0, 0, 0, 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"GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", 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+    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", 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diff --git a/tools/chewbbaca/test-data/allelecall_report_annot.html b/tools/chewbbaca/test-data/allelecall_report_annot.html
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@@ -0,0 +1,16 @@
+
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>AlleleCall Report - React Edition</title>
+</head>
+<body style="background-color: #f6f6f6">
+    <noscript> You need to enable JavaScript to run this app. </noscript>
+    <div id="root"></div>
+    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", 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"http://purl.uniprot.org/uniprot/Q8E2G4", "", "", "", "", ""], ["GCA-000007265-protein106", "GCA_000007265", "AE009948.1", "110766", "111524", "106", "1", "pyridoxal kinase", "http://purl.uniprot.org/uniprot/Q8E7Q4", "", "", "", "", ""], ["GCA-000007265-protein37", "GCA_000007265", "AE009948.1", "51221", "52108", "37", "1", "ABC transmembrane type-1 domain-containing protein", "http://purl.uniprot.org/uniprot/Q8E7W1", "", "", "", "", ""], ["GCA-000007265-protein5", "GCA_000007265", "AE009948.1", "4114", "4317", "5", "1", "Gbs0005 protein", "http://purl.uniprot.org/uniprot/Q8E7Z0", "", "", "", "", ""], ["GCA-000007265-protein71", "GCA_000007265", "AE009948.1", "81916", "82221", "71", "1", "Large ribosomal subunit protein uL24", "http://purl.uniprot.org/uniprot/Q3K3V8", "", "", "", "", ""], ["GCA-000007265-protein68", "GCA_000007265", "AE009948.1", "80951", "81157", "68", "1", "Large ribosomal subunit protein uL29", "http://purl.uniprot.org/uniprot/A2RC22", "", "", "", "", ""], ["GCA-000007265-protein47", "GCA_000007265", "AE009948.1", "60012", "61103", "47", "1", "N5-carboxyaminoimidazole ribonucleotide synthase", "http://purl.uniprot.org/uniprot/A0A0E1EJA7", "", "", "", "", ""], ["GCA-000007265-protein99", "GCA_000007265", "AE009948.1", "102830", "103405", "99", "1", "Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain-containing protein", "http://purl.uniprot.org/uniprot/Q8E7R0", "", "", "", "", ""], ["GCA-000007265-protein102", "GCA_000007265", "AE009948.1", "105338", "107167", "102", "1", "Chaperone protein DnaK", "http://purl.uniprot.org/uniprot/P0A3J2", "", "", "", "", ""], ["GCA-000007265-protein96", "GCA_000007265", "AE009948.1", "100791", "101270", "96", "1", "Competence-specific sigma factor ComX", "http://purl.uniprot.org/uniprot/Q8E7R3", "", "", "", "", ""], ["GCA-000007265-protein66", "GCA_000007265", "AE009948.1", "79871", "80524", "66", "1", "Small ribosomal subunit protein uS3", "http://purl.uniprot.org/uniprot/A2RC20", "", "", "", "", ""], ["GCA-000007265-protein20", "GCA_000007265", "AE009948.1", "30369", "31337", "20", "1", "Ribose-phosphate pyrophosphokinase 1", "http://purl.uniprot.org/uniprot/Q8E2H0", "", "", "", "", ""], ["GCA-000007265-protein57", "GCA_000007265", "AE009948.1", "73207", "74697", "57", "1", "Threonine synthase", "http://purl.uniprot.org/uniprot/A0A0E1EJC0", "", "", "", "", ""], ["GCA-000007265-protein42", "GCA_000007265", "AE009948.1", "55017", "55898", "42", "1", "N-acetylmannosamine kinase", "http://purl.uniprot.org/uniprot/A0A0E1EJA4", "", "", "", "", ""], ["GCA-000007265-protein14", "GCA_000007265", "AE009948.1", "13935", "15911", "14", "1", "ATP-dependent zinc metalloprotease FtsH", "http://purl.uniprot.org/uniprot/Q8E7Y0", "", "", "", "", ""], ["GCA-000007265-protein76", "GCA_000007265", "AE009948.1", "84290", "84646", "76", "1", "Large ribosomal subunit protein uL18", "http://purl.uniprot.org/uniprot/Q3K3V3", "", "", "", "", ""], ["GCA-000007265-protein98", "GCA_000007265", "AE009948.1", "102081", "102833", "98", "1", "Peptidase M15B domain-containing protein", "http://purl.uniprot.org/uniprot/Q8E7R1", "", "", "", "", ""], ["GCA-000007265-protein64", "GCA_000007265", "AE009948.1", "79220", "79498", "64", "1", "Small ribosomal subunit protein uS19", "http://purl.uniprot.org/uniprot/Q1JE54", "", "", "", "", ""], ["GCA-000007265-protein52", "GCA_000007265", "AE009948.1", "66381", "66818", "52", "1", "protein-tyrosine-phosphatase", "http://purl.uniprot.org/uniprot/A0A0E1EJB3", "", "", "", "", ""], ["GCA-000007265-protein10", "GCA_000007265", "AE009948.1", "10295", "10666", "10", "1", "Cell division protein DivIC", "http://purl.uniprot.org/uniprot/Q8E7Y5", "", "", "", "", ""]]}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265:0.000000000);\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>
+    <script src="./report_bundle.js"></script>
+</body>
+</html>
+
diff --git a/tools/chewbbaca/test-data/results_alleles2.tsv b/tools/chewbbaca/test-data/results_alleles2.tsv
new file mode 100644
index 00000000000..4c3aa74747d
--- /dev/null
+++ b/tools/chewbbaca/test-data/results_alleles2.tsv
@@ -0,0 +1,2 @@
+FILE	GCA-000007265-protein1	GCA-000007265-protein10	GCA-000007265-protein100	GCA-000007265-protein101	GCA-000007265-protein102	GCA-000007265-protein103	GCA-000007265-protein104	GCA-000007265-protein105	GCA-000007265-protein106	GCA-000007265-protein107	GCA-000007265-protein108	GCA-000007265-protein109	GCA-000007265-protein11	GCA-000007265-protein110	GCA-000007265-protein111	GCA-000007265-protein112	GCA-000007265-protein113	GCA-000007265-protein114	GCA-000007265-protein12	GCA-000007265-protein13	GCA-000007265-protein14	GCA-000007265-protein16	GCA-000007265-protein19	GCA-000007265-protein2	GCA-000007265-protein20	GCA-000007265-protein21	GCA-000007265-protein22	GCA-000007265-protein23	GCA-000007265-protein24	GCA-000007265-protein25	GCA-000007265-protein26	GCA-000007265-protein27	GCA-000007265-protein28	GCA-000007265-protein29	GCA-000007265-protein3	GCA-000007265-protein30	GCA-000007265-protein31	GCA-000007265-protein32	GCA-000007265-protein33	GCA-000007265-protein34	GCA-000007265-protein35	GCA-000007265-protein36	GCA-000007265-protein37	GCA-000007265-protein38	GCA-000007265-protein39	GCA-000007265-protein40	GCA-000007265-protein41	GCA-000007265-protein42	GCA-000007265-protein43	GCA-000007265-protein44	GCA-000007265-protein45	GCA-000007265-protein46	GCA-000007265-protein47	GCA-000007265-protein48	GCA-000007265-protein49	GCA-000007265-protein5	GCA-000007265-protein50	GCA-000007265-protein51	GCA-000007265-protein52	GCA-000007265-protein53	GCA-000007265-protein54	GCA-000007265-protein55	GCA-000007265-protein56	GCA-000007265-protein57	GCA-000007265-protein58	GCA-000007265-protein59	GCA-000007265-protein6	GCA-000007265-protein60	GCA-000007265-protein61	GCA-000007265-protein62	GCA-000007265-protein63	GCA-000007265-protein64	GCA-000007265-protein65	GCA-000007265-protein66	GCA-000007265-protein67	GCA-000007265-protein68	GCA-000007265-protein69	GCA-000007265-protein7	GCA-000007265-protein70	GCA-000007265-protein71	GCA-000007265-protein72	GCA-000007265-protein74	GCA-000007265-protein75	GCA-000007265-protein76	GCA-000007265-protein77	GCA-000007265-protein79	GCA-000007265-protein8	GCA-000007265-protein80	GCA-000007265-protein81	GCA-000007265-protein82	GCA-000007265-protein84	GCA-000007265-protein85	GCA-000007265-protein86	GCA-000007265-protein87	GCA-000007265-protein9	GCA-000007265-protein93	GCA-000007265-protein94	GCA-000007265-protein95	GCA-000007265-protein96	GCA-000007265-protein97	GCA-000007265-protein98	GCA-000007265-protein99
+GCA_000007265	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	NIPHEM	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
diff --git a/tools/chewbbaca/test-data/results_statistics.tsv b/tools/chewbbaca/test-data/results_statistics.tsv
index fcaedfc16f9..080d9316e42 100644
--- a/tools/chewbbaca/test-data/results_statistics.tsv
+++ b/tools/chewbbaca/test-data/results_statistics.tsv
@@ -1,2 +1,2 @@
 FILE	EXC	INF	PLOT3	PLOT5	LOTSC	NIPH	NIPHEM	ALM	ASM	PAMA	LNF	Invalid CDSs	Classified_CDSs	Total_CDSs
-GCA_000007265	101	0	0	0	0	0	1	0	0	0	0	10	104	114
+GCA_000007265	101	0	0	0	0	0	1	0	0	0	0	0	104	114
diff --git a/tools/chewbbaca/test-data/schema_seed_annotations.tsv b/tools/chewbbaca/test-data/schema_seed_annotations.tsv
new file mode 100644
index 00000000000..0755e3bc8eb
--- /dev/null
+++ b/tools/chewbbaca/test-data/schema_seed_annotations.tsv
@@ -0,0 +1,103 @@
+Locus	Genome	Contig	Start	Stop	Protein_ID	Coding_Strand	Uniprot_Name	UniProt_URL	Proteome_ID	Proteome_Product	Proteome_Gene_Name	Proteome_Species	Proteome_BSR
+GCA-000007265-protein111	GCA_000007265	AE009948.1	115072	115647	111	1	Probable DNA-directed RNA polymerase subunit delta	http://purl.uniprot.org/uniprot/Q3K3S3					
+GCA-000007265-protein25	GCA_000007265	AE009948.1	35393	35632	25	1	Acyl carrier protein	http://purl.uniprot.org/uniprot/Q8E7X3					
+GCA-000007265-protein101	GCA_000007265	AE009948.1	104624	105157	101	1	Protein GrpE	http://purl.uniprot.org/uniprot/Q3K3T3					
+GCA-000007265-protein31	GCA_000007265	AE009948.1	43963	44715	31	1	N-acetyltransferase domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7W7					
+GCA-000007265-protein79	GCA_000007265	AE009948.1	85478	85918	79	1	Large ribosomal subunit protein uL15	http://purl.uniprot.org/uniprot/Q3K3V0					
+GCA-000007265-protein108	GCA_000007265	AE009948.1	111995	112564	108	1	UPF0340 protein SAK_0153	http://purl.uniprot.org/uniprot/Q3K3S6					
+GCA-000007265-protein58	GCA_000007265	AE009948.1	74802	76082	58	1	Probable multidrug resistance protein NorM	http://purl.uniprot.org/uniprot/A0A0E1EEL2					
+GCA-000007265-protein32	GCA_000007265	AE009948.1	44735	46282	32	1	Bifunctional purine biosynthesis protein PurH	http://purl.uniprot.org/uniprot/P67545					
+GCA-000007265-protein69	GCA_000007265	AE009948.1	81183	81443	69	1	Small ribosomal subunit protein uS17	http://purl.uniprot.org/uniprot/B5XJ45					
+GCA-000007265-protein80	GCA_000007265	AE009948.1	85939	87243	80	1	Protein translocase subunit SecY	http://purl.uniprot.org/uniprot/Q8E7S1					
+GCA-000007265-protein62	GCA_000007265	AE009948.1	77974	78270	62	1	Large ribosomal subunit protein uL23	http://purl.uniprot.org/uniprot/Q8E7T6					
+GCA-000007265-protein8	GCA_000007265	AE009948.1	6248	9745	8	1	Transcription-repair-coupling factor	http://purl.uniprot.org/uniprot/Q8E7Y7					
+GCA-000007265-protein28	GCA_000007265	AE009948.1	40720	42174	28	1	Amidophosphoribosyltransferase	http://purl.uniprot.org/uniprot/A0A8I2JU49					
+GCA-000007265-protein113	GCA_000007265	AE009948.1	117633	118559	113	1	AB hydrolase-1 domain-containing protein	http://purl.uniprot.org/uniprot/Q8E289					
+GCA-000007265-protein107	GCA_000007265	AE009948.1	111534	111998	107	1	ECF transporter S component	http://purl.uniprot.org/uniprot/A0A1F0CHU0					
+GCA-000007265-protein46	GCA_000007265	AE009948.1	59588	60025	46	1	N5-carboxyaminoimidazole ribonucleotide mutase	http://purl.uniprot.org/uniprot/A0A380JAU3					
+GCA-000007265-protein35	GCA_000007265	AE009948.1	49072	49770	35	1	Putative N-acetylmannosamine-6-phosphate 2-epimerase	http://purl.uniprot.org/uniprot/P65518					
+GCA-000007265-protein43	GCA_000007265	AE009948.1	55906	56883	43	1	Alpha/beta fold hydrolase	http://purl.uniprot.org/uniprot/A0A0E1EEK2					
+GCA-000007265-protein67	GCA_000007265	AE009948.1	80528	80941	67	1	Large ribosomal subunit protein uL16	http://purl.uniprot.org/uniprot/Q3K3W2					
+GCA-000007265-protein94	GCA_000007265	AE009948.1	99401	99952	94	1	Prolyl-tRNA synthetase	http://purl.uniprot.org/uniprot/Q8E2A6					
+GCA-000007265-protein75	GCA_000007265	AE009948.1	83653	84189	75	1	Large ribosomal subunit protein uL6	http://purl.uniprot.org/uniprot/Q8E2B9					
+GCA-000007265-protein36	GCA_000007265	AE009948.1	49817	51133	36	1	Uncharacterized protein	http://purl.uniprot.org/uniprot/Q8E7W2					
+GCA-000007265-protein59	GCA_000007265	AE009948.1	76288	76596	59	1	Small ribosomal subunit protein uS10	http://purl.uniprot.org/uniprot/A2RC13					
+GCA-000007265-protein30	GCA_000007265	AE009948.1	43392	43940	30	1	Phosphoribosylglycinamide formyltransferase	http://purl.uniprot.org/uniprot/A0A8I2FG92					
+GCA-000007265-protein34	GCA_000007265	AE009948.1	47521	48825	34	1	LysM domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7W4					
+GCA-000007265-protein6	GCA_000007265	AE009948.1	4477	5592	6	1	Ribosome-binding ATPase YchF	http://purl.uniprot.org/uniprot/Q8E7Y9					
+GCA-000007265-protein87	GCA_000007265	AE009948.1	90239	90625	87	1	Large ribosomal subunit protein bL17	http://purl.uniprot.org/uniprot/Q3K3U3					
+GCA-000007265-protein51	GCA_000007265	AE009948.1	65231	66229	51	1	Holliday junction branch migration complex subunit RuvB	http://purl.uniprot.org/uniprot/Q8E2D9					
+GCA-000007265-protein103	GCA_000007265	AE009948.1	107456	108595	103	1	Chaperone protein DnaJ	http://purl.uniprot.org/uniprot/Q8E298					
+GCA-000007265-protein12	GCA_000007265	AE009948.1	12091	13365	12	1	tRNA(Ile)-lysidine synthase	http://purl.uniprot.org/uniprot/Q8E2H4					
+GCA-000007265-protein97	GCA_000007265	AE009948.1	101392	102084	97	1	Phosphoglycerate mutase	http://purl.uniprot.org/uniprot/A0A076YUP2					
+GCA-000007265-protein86	GCA_000007265	AE009948.1	89286	90224	86	1	DNA-directed RNA polymerase subunit alpha	http://purl.uniprot.org/uniprot/Q8CX32					
+GCA-000007265-protein104	GCA_000007265	AE009948.1	108709	109956	104	1	PLP-dependent aminotransferase family protein	http://purl.uniprot.org/uniprot/A0A0E1EJF9					
+GCA-000007265-protein24	GCA_000007265	AE009948.1	34390	35382	24	1	Phosphate acyltransferase	http://purl.uniprot.org/uniprot/P65740					
+GCA-000007265-protein100	GCA_000007265	AE009948.1	103548	104582	100	1	Heat-inducible transcription repressor HrcA	http://purl.uniprot.org/uniprot/Q8E2A0					
+GCA-000007265-protein1	GCA_000007265	AE009948.1	54	1463	1	1	Chromosomal replication initiator protein DnaA	http://purl.uniprot.org/uniprot/A0A0K0MXQ6					
+GCA-000007265-protein27	GCA_000007265	AE009948.1	36583	40308	27	1	Phosphoribosylformylglycinamidine synthase	http://purl.uniprot.org/uniprot/A0A8I2JTY4					
+GCA-000007265-protein82	GCA_000007265	AE009948.1	88092	88310	82	1	Translation initiation factor IF-1	http://purl.uniprot.org/uniprot/A2RC36					
+GCA-000007265-protein61	GCA_000007265	AE009948.1	77351	77974	61	1	Large ribosomal subunit protein uL4	http://purl.uniprot.org/uniprot/Q3K3W8					
+GCA-000007265-protein109	GCA_000007265	AE009948.1	112601	113443	109	-1	Mechanosensitive ion channel family protein	http://purl.uniprot.org/uniprot/Q8E293					
+GCA-000007265-protein74	GCA_000007265	AE009948.1	83145	83543	74	1	Small ribosomal subunit protein uS8	http://purl.uniprot.org/uniprot/Q8E2C0					
+GCA-000007265-protein110	GCA_000007265	AE009948.1	113600	114883	110	1	Trigger factor	http://purl.uniprot.org/uniprot/Q8E292					
+GCA-000007265-protein93	GCA_000007265	AE009948.1	98822	99082	93	-1							
+GCA-000007265-protein72	GCA_000007265	AE009948.1	82245	82787	72	1	Large ribosomal subunit protein uL5	http://purl.uniprot.org/uniprot/Q3K3V7					
+GCA-000007265-protein84	GCA_000007265	AE009948.1	88470	88835	84	1	Small ribosomal subunit protein uS13	http://purl.uniprot.org/uniprot/P66390					
+GCA-000007265-protein19	GCA_000007265	AE009948.1	28902	30245	19	1	PcsB protein	http://purl.uniprot.org/uniprot/Q8E7X9					
+GCA-000007265-protein65	GCA_000007265	AE009948.1	79514	79858	65	1	Large ribosomal subunit protein uL22	http://purl.uniprot.org/uniprot/Q3K3W4					
+GCA-000007265-protein49	GCA_000007265	AE009948.1	62573	63871	49	1	Adenylosuccinate lyase	http://purl.uniprot.org/uniprot/A0A0E1EEW4					
+GCA-000007265-protein55	GCA_000007265	AE009948.1	69250	71892	55	1	Aldehyde-alcohol dehydrogenase	http://purl.uniprot.org/uniprot/Q8E7U2					
+GCA-000007265-protein41	GCA_000007265	AE009948.1	54083	55000	41	1	N-acetylneuraminate lyase	http://purl.uniprot.org/uniprot/A0A076Z407					
+GCA-000007265-protein85	GCA_000007265	AE009948.1	88853	89236	85	1	Small ribosomal subunit protein uS11	http://purl.uniprot.org/uniprot/A2RC39					
+GCA-000007265-protein70	GCA_000007265	AE009948.1	81468	81836	70	1	Large ribosomal subunit protein uL14	http://purl.uniprot.org/uniprot/A2RC24					
+GCA-000007265-protein22	GCA_000007265	AE009948.1	32610	33371	22	1	DNA repair protein RecO	http://purl.uniprot.org/uniprot/Q8E2G8					
+GCA-000007265-protein112	GCA_000007265	AE009948.1	115920	117524	112	1	CTP synthase	http://purl.uniprot.org/uniprot/Q8E290					
+GCA-000007265-protein23	GCA_000007265	AE009948.1	33434	34312	23	1	CAAX protease	http://purl.uniprot.org/uniprot/A0A1F0CHG3					
+GCA-000007265-protein77	GCA_000007265	AE009948.1	84665	85159	77	1	Small ribosomal subunit protein uS5	http://purl.uniprot.org/uniprot/Q3K3V2					
+GCA-000007265-protein54	GCA_000007265	AE009948.1	67202	68980	54	1	Acetyltransferase family protein, putative	http://purl.uniprot.org/uniprot/A0A0E1EEX2					
+GCA-000007265-protein9	GCA_000007265	AE009948.1	10036	10308	9	1	RNA-binding S4 domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7Y6					
+GCA-000007265-protein39	GCA_000007265	AE009948.1	52961	53404	39	1	YhcH/YjgK/YiaL family protein	http://purl.uniprot.org/uniprot/Q8E7V9					
+GCA-000007265-protein50	GCA_000007265	AE009948.1	64023	64934	50	1	Helix-turn-helix domain-containing protein	http://purl.uniprot.org/uniprot/A0A0E1EEL0					
+GCA-000007265-protein44	GCA_000007265	AE009948.1	56906	57709	44	-1	Sialic acid utilization regulator, RpiR family	http://purl.uniprot.org/uniprot/A0A0E1EEW0					
+GCA-000007265-protein13	GCA_000007265	AE009948.1	13370	13912	13	1	Hypoxanthine-guanine phosphoribosyltransferase	http://purl.uniprot.org/uniprot/Q8E2H3					
+GCA-000007265-protein95	GCA_000007265	AE009948.1	100172	100591	95	1	DUF2992 domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7R4					
+GCA-000007265-protein105	GCA_000007265	AE009948.1	110027	110803	105	1	tRNA pseudouridine synthase A	http://purl.uniprot.org/uniprot/Q8CX20					
+GCA-000007265-protein2	GCA_000007265	AE009948.1	1618	2754	2	1	Beta sliding clamp	http://purl.uniprot.org/uniprot/Q8E7Z3					
+GCA-000007265-protein29	GCA_000007265	AE009948.1	42202	43224	29	1	Phosphoribosylformylglycinamidine cyclo-ligase	http://purl.uniprot.org/uniprot/Q8E2G1					
+GCA-000007265-protein60	GCA_000007265	AE009948.1	76701	77327	60	1	Large ribosomal subunit protein uL3	http://purl.uniprot.org/uniprot/Q3K3W9					
+GCA-000007265-protein48	GCA_000007265	AE009948.1	61157	62548	48	1	Beta-carotene 15,15'-monooxygenase	http://purl.uniprot.org/uniprot/A0A1F0CGC5					
+GCA-000007265-protein114	GCA_000007265	AE009948.1	118754	119200	114	1	dUTP diphosphatase	http://purl.uniprot.org/uniprot/A0A0H1FVA3					
+GCA-000007265-protein45	GCA_000007265	AE009948.1	57991	59256	45	1	Phosphoribosylamine--glycine ligase	http://purl.uniprot.org/uniprot/A0A0E1EEK4					
+GCA-000007265-protein21	GCA_000007265	AE009948.1	31334	32620	21	1							
+GCA-000007265-protein81	GCA_000007265	AE009948.1	87338	87976	81	1	Adenylate kinase	http://purl.uniprot.org/uniprot/P65203					
+GCA-000007265-protein33	GCA_000007265	AE009948.1	46475	47374	33	1	Peptidase M23 domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7W5					
+GCA-000007265-protein38	GCA_000007265	AE009948.1	52118	52948	38	1	ABC transmembrane type-1 domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7W0					
+GCA-000007265-protein11	GCA_000007265	AE009948.1	10803	12089	11	1	beta-lactamase	http://purl.uniprot.org/uniprot/Q8E7Y3					
+GCA-000007265-protein40	GCA_000007265	AE009948.1	53424	54086	40	1	Beta-carotene 15,15'-monooxygenase	http://purl.uniprot.org/uniprot/A0A1F0CI38					
+GCA-000007265-protein56	GCA_000007265	AE009948.1	72071	73087	56	1	Alcohol dehydrogenase	http://purl.uniprot.org/uniprot/X5K0V4					
+GCA-000007265-protein3	GCA_000007265	AE009948.1	2812	3705	3	1	diacylglycerol kinase family protein	http://purl.uniprot.org/uniparc/UPI0002BB2C63					
+GCA-000007265-protein7	GCA_000007265	AE009948.1	5676	6251	7	1	Peptidyl-tRNA hydrolase	http://purl.uniprot.org/uniprot/Q8E2I1					
+GCA-000007265-protein53	GCA_000007265	AE009948.1	66825	67205	53	1	MORN motif family protein	http://purl.uniprot.org/uniprot/A0A1F0CHD6					
+GCA-000007265-protein16	GCA_000007265	AE009948.1	20579	20866	16	1	RNAase	http://purl.uniprot.org/uniprot/U5P1X6					
+GCA-000007265-protein63	GCA_000007265	AE009948.1	78288	79121	63	1	Large ribosomal subunit protein uL2	http://purl.uniprot.org/uniprot/Q3K3W6					
+GCA-000007265-protein26	GCA_000007265	AE009948.1	35756	36460	26	1	Phosphoribosylaminoimidazole-succinocarboxamide synthase	http://purl.uniprot.org/uniprot/Q8E2G4					
+GCA-000007265-protein106	GCA_000007265	AE009948.1	110766	111524	106	1	pyridoxal kinase	http://purl.uniprot.org/uniprot/Q8E7Q4					
+GCA-000007265-protein37	GCA_000007265	AE009948.1	51221	52108	37	1	ABC transmembrane type-1 domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7W1					
+GCA-000007265-protein5	GCA_000007265	AE009948.1	4114	4317	5	1	Gbs0005 protein	http://purl.uniprot.org/uniprot/Q8E7Z0					
+GCA-000007265-protein71	GCA_000007265	AE009948.1	81916	82221	71	1	Large ribosomal subunit protein uL24	http://purl.uniprot.org/uniprot/Q3K3V8					
+GCA-000007265-protein68	GCA_000007265	AE009948.1	80951	81157	68	1	Large ribosomal subunit protein uL29	http://purl.uniprot.org/uniprot/A2RC22					
+GCA-000007265-protein47	GCA_000007265	AE009948.1	60012	61103	47	1	N5-carboxyaminoimidazole ribonucleotide synthase	http://purl.uniprot.org/uniprot/A0A0E1EJA7					
+GCA-000007265-protein99	GCA_000007265	AE009948.1	102830	103405	99	1	Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7R0					
+GCA-000007265-protein102	GCA_000007265	AE009948.1	105338	107167	102	1	Chaperone protein DnaK	http://purl.uniprot.org/uniprot/P0A3J2					
+GCA-000007265-protein96	GCA_000007265	AE009948.1	100791	101270	96	1	Competence-specific sigma factor ComX	http://purl.uniprot.org/uniprot/Q8E7R3					
+GCA-000007265-protein66	GCA_000007265	AE009948.1	79871	80524	66	1	Small ribosomal subunit protein uS3	http://purl.uniprot.org/uniprot/A2RC20					
+GCA-000007265-protein20	GCA_000007265	AE009948.1	30369	31337	20	1	Ribose-phosphate pyrophosphokinase 1	http://purl.uniprot.org/uniprot/Q8E2H0					
+GCA-000007265-protein57	GCA_000007265	AE009948.1	73207	74697	57	1	Threonine synthase	http://purl.uniprot.org/uniprot/A0A0E1EJC0					
+GCA-000007265-protein42	GCA_000007265	AE009948.1	55017	55898	42	1	N-acetylmannosamine kinase	http://purl.uniprot.org/uniprot/A0A0E1EJA4					
+GCA-000007265-protein14	GCA_000007265	AE009948.1	13935	15911	14	1	ATP-dependent zinc metalloprotease FtsH	http://purl.uniprot.org/uniprot/Q8E7Y0					
+GCA-000007265-protein76	GCA_000007265	AE009948.1	84290	84646	76	1	Large ribosomal subunit protein uL18	http://purl.uniprot.org/uniprot/Q3K3V3					
+GCA-000007265-protein98	GCA_000007265	AE009948.1	102081	102833	98	1	Peptidase M15B domain-containing protein	http://purl.uniprot.org/uniprot/Q8E7R1					
+GCA-000007265-protein64	GCA_000007265	AE009948.1	79220	79498	64	1	Small ribosomal subunit protein uS19	http://purl.uniprot.org/uniprot/Q1JE54					
+GCA-000007265-protein52	GCA_000007265	AE009948.1	66381	66818	52	1	protein-tyrosine-phosphatase	http://purl.uniprot.org/uniprot/A0A0E1EJB3					
+GCA-000007265-protein10	GCA_000007265	AE009948.1	10295	10666	10	1	Cell division protein DivIC	http://purl.uniprot.org/uniprot/Q8E7Y5					

From e06d66e3970fea0eba5d2f13a19226b3abffb32d Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 3 Apr 2024 13:23:40 +0200
Subject: [PATCH 51/97] updated test of DownloadSchema.xml

---
 tools/chewbbaca/DownloadSchema.xml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
index 4f7e1328303..30dfcd24e8f 100644
--- a/tools/chewbbaca/DownloadSchema.xml
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -39,10 +39,13 @@
         <data format="zip" name="schema" from_work_dir="schema_seed.zip" label="${tool.name} Schema files"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_exit_code="0">
             <param name="species_id" value="13"/>
             <param name="schema_id" value="1"/>
-            <output name="schema" file="Download_C-chauvoei_seed.zip" compare="sim_size"/>
+            <assert_stdout>
+                <has_text text="Schema is now available at"/>
+                <has_text text="Finished at"/>
+            </assert_stdout>
         </test>
     </tests>
     <help>

From b5d53ff4aa1bc90ecccc1d41874a821aba9d26d7 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 3 Apr 2024 14:34:49 +0200
Subject: [PATCH 52/97] updated test-data

---
 ...007265.1_ASM726v1_PExternalschema_seed.zip | Bin 115704 -> 115704 bytes
 .../GCA_000007265.1_ASM726v1_schema_seed.zip  | Bin 115704 -> 115704 bytes
 ...A_000007265.1_ASM726v1_schema_seed_trn.zip | Bin 0 -> 144041 bytes
 3 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed_trn.zip

diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip
index 5106c0d45882189858b6f782783b6bfa04b82ffb..cf7f5df326a9aedad6f93321513a7a76a2f95c90 100644
GIT binary patch
delta 9195
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delta 9195
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diff --git a/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip b/tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
index ffd5a982bd4943cc503a9e71666e99eea923b19b..14332e5b569c014675848ca0bf6b39f8a264108f 100644
GIT binary patch
delta 9195
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delta 9195
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zAaMWb{{RjL9hM7=YZw86`%l9Fa5!i`0W9v$C<xqtYT$#zK}UGN;@HMO;QmvW9vlwZ
k-vx^!8V7;<Pj&SF9S#Mk7>$7N4)|vc6h~p6I8Q|RUpeOui2wiq

literal 0
HcmV?d00001


From 559ae100369c4831b0aec97c939b9e38ac33d3be Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 3 Apr 2024 14:35:08 +0200
Subject: [PATCH 53/97] updated test-data

---
 tools/chewbbaca/test-data/NSStats.txt | 39 +++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/tools/chewbbaca/test-data/NSStats.txt b/tools/chewbbaca/test-data/NSStats.txt
index e69de29bb2d..6b96ee40a50 100644
--- a/tools/chewbbaca/test-data/NSStats.txt
+++ b/tools/chewbbaca/test-data/NSStats.txt
@@ -0,0 +1,39 @@
+
+chewBBACA version: 3.3.3
+Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
+Github: https://github.com/B-UMMI/chewBBACA
+Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
+Contacts: imm-bioinfo@medicina.ulisboa.pt
+
+=======================
+  chewBBACA - NSStats
+=======================
+Started at: 2024-04-03T10:24:19
+
+
+Retrieving data...
+
+------------------------------------------------------------------------------
+Species                             id       #schemas     #loci      #alleles 
+------------------------------------------------------------------------------
+Streptococcus pyogenes              1           1          3044       398511  
+Acinetobacter baumannii             2           1          2390       701606  
+Arcobacter butzleri                 3           1          7474       82419   
+Campylobacter jejuni                4           1          2794       299214  
+Escherichia coli                    5           1          7601      2963736  
+Listeria monocytogenes              6           1          1748       371020  
+Yersinia enterocolitica             7           1          6344       154555  
+Salmonella enterica                 8           1          8558      2879459  
+Streptococcus agalactiae            9           1          3641       248987  
+Brucella melitensis                 10          1          2762       11222   
+Brucella                            11          1          1764       78557   
+Clostridium perfringens             12          1          1431       152324  
+Clostridium chauvoei                13          1          2223        7711   
+Bacillus anthracis                  14          1          3803       52474   
+Klebsiella oxytoca                  15          1          4201       132939  
+Clostridium neonatale               16          1          2350       13115   
+------------------------------------------------------------------------------
+
+
+Finished at: 2024-04-03T10:24:23
+Took  0m 4s.

From 3ff76771e158557b72502eef565d1fa720605c16 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 3 Apr 2024 14:36:58 +0200
Subject: [PATCH 54/97] update on test and output of ExtractCgMLST.xml

---
 tools/chewbbaca/ExtractCgMLST.xml | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/ExtractCgMLST.xml b/tools/chewbbaca/ExtractCgMLST.xml
index 57c0403a8e2..47bca4a1479 100644
--- a/tools/chewbbaca/ExtractCgMLST.xml
+++ b/tools/chewbbaca/ExtractCgMLST.xml
@@ -17,8 +17,7 @@
         #if str($genomes2remove) != 'None'
             --g $genomes2remove
         #end if 
-        -i './input/results_alleles.tsv' -o './output' &&
-    zip -r ExtractCgMLST.zip './output'
+        -i 'input/results_alleles.tsv' -o 'output'
     ]]></command>
     <inputs>
         <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
@@ -31,7 +30,9 @@
         </section>
     </inputs>
     <outputs>
-        <data format="zip" name="ExtractCgMLST" from_work_dir="ExtractCgMLST.zip" label="${tool.name} on ${on_string}: ExtractCgMLST files"/>
+        <collection name="output_collection" type="list" format="html,tsv,txt" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="__name_and_ext__" directory="output"/>
+        </collection>
     </outputs>
     <tests>
         <test>
@@ -40,7 +41,18 @@
                     <element name="results_alleles" value="results_alleles.tsv" ftype="tabular"/>
                 </collection>
             </param>
-            <output name="ExtractCgMLST" file="ExtractCgMLST.zip" compare="sim_size"/>
+            <output_collection name="output_collection" type="list">
+                <element name="missing_loci_stats">
+                    <assert_contents>
+                        <has_text_matching expression="GCA_000007265"/>
+                    </assert_contents>
+                </element>
+                <element name="presence_absence">
+                    <assert_contents>
+                        <has_text_matching expression="GCA_000007265"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
     </tests>
     <help>

From 8008177dc35fbbedc6ab92984eae78ed7d4df959 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Fri, 5 Apr 2024 10:44:16 +0200
Subject: [PATCH 55/97] Update tools/chewbbaca/AlleleCall.xml

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>
---
 tools/chewbbaca/AlleleCall.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 1fdb75b1549..9224446abd2 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -56,7 +56,7 @@
         <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
             <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
-            <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" help="By default, gets the training file from the schema"/>
             <param argument="--cds-input" type="data" format="txt" label="CDS input" optional="true" />
             <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="" optional="true" label="BLAST Score Ratio value" /> 
             <param argument="--minimum-length" type="integer" min="0" value="" optional="true" label="Minimum sequence length value"/>

From 5f5f26109da33cb31a4b8e1532ad9d886639f95d Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Fri, 5 Apr 2024 12:29:28 +0200
Subject: [PATCH 56/97] Update tools/chewbbaca/AlleleCall.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/chewbbaca/AlleleCall.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 9224446abd2..951d209200b 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -8,7 +8,7 @@
         mkdir './input' &&
         mkdir './schema' &&
         #for $file in $input_file
-        ln -sf $file './input/${file.element_identifier}' &&
+        ln -sf '$file' './input/${file.element_identifier}' &&
         #end for
         unzip $input_schema -d './schema' &&
         chewBBACA.py AlleleCall

From d7650b9c349e794c1dadb6251b5fd3be1477c704 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Fri, 5 Apr 2024 12:32:44 +0200
Subject: [PATCH 57/97] Update tools/chewbbaca/AlleleCall.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/chewbbaca/AlleleCall.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 951d209200b..6d8eb2a1425 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -10,7 +10,7 @@
         #for $file in $input_file
         ln -sf '$file' './input/${file.element_identifier}' &&
         #end for
-        unzip $input_schema -d './schema' &&
+        unzip '$input_schema' -d './schema' &&
         chewBBACA.py AlleleCall
             #if str($training_file) != 'None'
                 --ptf $training_file

From e1199b1784c50e7a56bd2699346eb9f7b5142903 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Fri, 5 Apr 2024 12:35:07 +0200
Subject: [PATCH 58/97] Update tools/chewbbaca/PrepExternalSchema.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/chewbbaca/PrepExternalSchema.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index fe9f919ee2c..10222289a51 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -12,7 +12,7 @@
                 --ptf '$training_file'
             #end if
             #if str($genes_list) != 'None'
-                --gl $genes_list
+                --gl '$genes_list'
             #end if    
             @INPUT@
             $size_filter

From 533811b0638b430a0b0ba434ab83447d801fa367 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Fri, 5 Apr 2024 12:36:15 +0200
Subject: [PATCH 59/97] Update tools/chewbbaca/AlleleCallEvaluator.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/chewbbaca/AlleleCallEvaluator.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index bfe4dd27978..d5fcd7316ea 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -21,7 +21,7 @@
             $no_tree
             $cg_alignment
             -i './input' -g './schema/schema_seed/' -o '${allelecall_report.files_path}' &&
-        cp '${allelecall_report.files_path}'/allelecall_report.html $allelecall_report
+        cp '${allelecall_report.files_path}/allelecall_report.html' '$allelecall_report'
     ]]></command>
     <inputs>
         <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>

From 9c534c8a864e8491b88b5e83813feedc5de826f1 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 13:16:56 +0200
Subject: [PATCH 60/97] added test for 3 optional outputs of AllelCall.xml

---
 tools/chewbbaca/AlleleCall.xml | 45 ++++++++++++++++++++++++----------
 1 file changed, 32 insertions(+), 13 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 6d8eb2a1425..e0c5f33ae2e 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -5,12 +5,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir './input' &&
-        mkdir './schema' &&
+        mkdir 'input' &&
+        mkdir 'schema' &&
         #for $file in $input_file
-        ln -sf '$file' './input/${file.element_identifier}' &&
+        ln -sf $file 'input/${file.element_identifier}' &&
         #end for
-        unzip '$input_schema' -d './schema' &&
+        unzip $input_schema -d 'schema' &&
         chewBBACA.py AlleleCall
             #if str($training_file) != 'None'
                 --ptf $training_file
@@ -47,9 +47,10 @@
                 --output-novel
             #end if
             #if 'hash_profile' in $output_selector:
-                --hash-profile 
+            ## It can use any hashing algorithm from hashlib but for simplicity we set it to md5
+                --hash-profile md5
             #end if
-            -i './input' -g './schema/schema_seed/' -o './output'
+            -i 'input' -g 'schema/schema_seed/' -o 'output'
     ]]></command>
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="true" label="Genome assemblies in FASTA format"/>
@@ -82,25 +83,25 @@
             <param name="output_selector" type="select" multiple="true" optional="true" display="checkboxes" label="Select / Deselect all">
                 <option value="output_unclassified">Create a Fasta file with unclassified coding sequences. (--output-unclassified)</option>
                 <option value="output_missing">Create a Fasta file with coding sequences classified as NIPH, NIPHEM, ASM, ALM, PLOT3, PLOT5 and LOTSC. (--output-missing)</option>
-                <option value="output_novel ">Create Fasta file with the novel alleles inferred during the allele calling. (--output-novel)</option>
-                <option value="hash_profile ">Create TSV file with hashed allelic profiles. (--hash-profile) </option>
+                <option value="output_novel">Create Fasta file with the novel alleles inferred during the allele calling. (--output-novel)</option>
+                <option value="hash_profile">Create TSV file with hashed allelic profiles. (--hash-profile) </option>
             </param>
         </section>
     </inputs>
     <outputs>
         <collection name="allelecall_results" type="list" label="${tool.name} on ${on_string}: AlleleCall Results">
-            <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="./output"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output"/>
         </collection>
         <collection name="allelcall_log" type="list" label="${tool.name} on ${on_string}: AlleleCall Logs">
-            <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" format="txt" directory="./output"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" format="txt" directory="output"/>
         </collection>
-        <data name="unclassified_fasta" format="fasta" from_work_dir="./output" label="${tool.name} on ${on_string}: Unclassified fasta">
+        <data name="unclassified_fasta" format="fasta" from_work_dir="output/unclassified_sequences.fasta" label="${tool.name} on ${on_string}: Unclassified fasta">
             <filter>output_selector['output_unclassified']</filter>
         </data>
-        <data name="missing_fasta" format="fasta" from_work_dir="./output" label="${tool.name} on ${on_string}: Missing fasta">
+        <data name="missing_fasta" format="fasta" from_work_dir="output/missing_classes.fasta" label="${tool.name} on ${on_string}: Missing fasta">
             <filter>output_selector['output_missing']</filter>
         </data>
-        <data name="novel_fasta" format="fasta" from_work_dir="./output" label="${tool.name} on ${on_string}: Novel fasta">
+        <data name="novel_fasta" format="fasta" from_work_dir="output/novel_alleles.fasta" label="${tool.name} on ${on_string}: Novel fasta">
             <filter>output_selector['output_novel']</filter>
         </data>
     </outputs>
@@ -108,6 +109,7 @@
         <test expect_num_outputs="5">
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <param name="output_selector" value="output_unclassified,output_missing,hash_profile" />
             <output_collection name="allelecall_results" type="list">
                 <element name="cds_coordinates" file="cds_coordinates.tsv" compare="sim_size"/>
                 <element name="loci_summary_stats" file="loci_summary_stats.tsv" compare="sim_size"/>
@@ -123,6 +125,12 @@
                     </assert_contents>
                 </element>
                 <element name="results_alleles" file="results_alleles.tsv" compare="sim_size"/>
+                <element name="results_alleles_hashed" ftype="tabular">
+                    <assert_contents>
+                        <has_text_matching expression="FILE.*GCA-000007265-protein1.*GCA-000007265-protein10.*GCA-000007265-protein100"/>
+                        <has_text_matching expression="GCA_000007265.*308e7666834338d0530d925b2737f2c6.*4aece26d201d59a90947e3400c7abf3f.*ebea148832aa2ae2704d37ebd5123169"/>
+                    </assert_contents>
+                </element>
                 <element name="results_statistics" file="results_statistics.tsv" compare="sim_size"/>
             </output_collection>
             <output_collection name="allelcall_log" type="list">
@@ -132,6 +140,17 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output name="unclassified_fasta">
+                <assert_contents>
+                    <has_text_matching expression="GCA_000007265-protein15"/>
+                    <has_text_matching expression="ATGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGATGTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAG"/>
+                </assert_contents>
+            </output>
+            <output name="missing_fasta">
+                <assert_contents>
+                    <has_text_matching expression="1|GCA_000007265|GCA-000007265-protein16&amp;NIPHEM|GCA_000007265-protein16&amp;EXC"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>

From 9bb69d207cd018831fdc7384089e6e4262199898 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 13:19:38 +0200
Subject: [PATCH 61/97] Update command line of JoinProfiles.xml

---
 tools/chewbbaca/JoinProfiles.xml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/tools/chewbbaca/JoinProfiles.xml b/tools/chewbbaca/JoinProfiles.xml
index 9780fdee590..159ffde8db4 100644
--- a/tools/chewbbaca/JoinProfiles.xml
+++ b/tools/chewbbaca/JoinProfiles.xml
@@ -5,14 +5,8 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        #set $profiles = $input1
-        #set $profile_tmp = []
-        #for $i, $k in enumerate($profiles)
-            ln -s '$k' './profile_${i}.tsv' &&
-            $profile_tmp.append("profile_" + str($i) + ".tsv")
-        #end for
         chewBBACA.py JoinProfiles
-            -p ${' '.join($profile_tmp)}
+            -p ${str($input1).replace(',', ' ')}
             -o JoinedProfile.tsv
             $common
     ]]></command>

From fd52c6e094145275e8ab9041f954300b2eb80cd2 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 13:30:09 +0200
Subject: [PATCH 62/97] corrected id of tools all lowercase with chewbbaca
 prefix

---
 tools/chewbbaca/AlleleCall.xml          | 2 +-
 tools/chewbbaca/AlleleCallEvaluator.xml | 2 +-
 tools/chewbbaca/CreateSchema.xml        | 2 +-
 tools/chewbbaca/DownloadSchema.xml      | 2 +-
 tools/chewbbaca/ExtractCgMLST.xml       | 2 +-
 tools/chewbbaca/JoinProfiles.xml        | 2 +-
 tools/chewbbaca/NSStats.xml             | 2 +-
 tools/chewbbaca/PrepExternalSchema.xml  | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index e0c5f33ae2e..b6a2296d7c6 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -1,4 +1,4 @@
-<tool id="AlleleCall" name="ChewBBACA AlleleCall" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="chewbbaca_allelecall" name="ChewBBACA AlleleCall" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Determine the allelic profiles of a set of genomes</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index d5fcd7316ea..9fe21050d20 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -1,4 +1,4 @@
-<tool id="AlleleCallEvaluator" name="chewBBACA AlleleCallEvaluator" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="chewbbaca_allelecallevaluator" name="chewBBACA AlleleCallEvaluator" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Build an interactive report for allele calling results evaluation</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 703d09f7629..d2995b2b70d 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -1,4 +1,4 @@
-<tool id="CreateSchema" name="chewBBACA CreateSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Create a gene-by-gene schema</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
index 30dfcd24e8f..7ac145d8296 100644
--- a/tools/chewbbaca/DownloadSchema.xml
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -1,4 +1,4 @@
-<tool id="DownloadSchema" name="chewBBACA DownloadSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="chewbbaca_downloadschema" name="chewBBACA DownloadSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Download a schema from Chewie-NS</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/chewbbaca/ExtractCgMLST.xml b/tools/chewbbaca/ExtractCgMLST.xml
index 47bca4a1479..12ca89987a7 100644
--- a/tools/chewbbaca/ExtractCgMLST.xml
+++ b/tools/chewbbaca/ExtractCgMLST.xml
@@ -1,4 +1,4 @@
-<tool id="ExtractCgMLST" name="chewBBACA ExtractCgMLST" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="chewbbaca_extractcgmlst" name="chewBBACA ExtractCgMLST" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Determine the set of loci that constitute the core genome</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/chewbbaca/JoinProfiles.xml b/tools/chewbbaca/JoinProfiles.xml
index 159ffde8db4..7d11e8a606f 100644
--- a/tools/chewbbaca/JoinProfiles.xml
+++ b/tools/chewbbaca/JoinProfiles.xml
@@ -1,4 +1,4 @@
-<tool id="JoinProfiles" name="chewBBACA JoinProfiles" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="chewbbaca_joinprofiles" name="chewBBACA JoinProfiles" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Join allele calling results from different runs</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index 07cfe4af552..c452bc6a755 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -1,4 +1,4 @@
-<tool id="NSStats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="chewbbaca_nsstats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Retrieve basic information about the species and schemas in Chewie-NS</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index 10222289a51..7fb47b81b7e 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -1,4 +1,4 @@
-<tool id="PrepExternalSchema" name="chewBBACA PrepExternalSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="prepexternalschema" name="chewBBACA PrepExternalSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Adapt an external schema to be used with chewBBACA</description>
     <macros>
         <import>macros.xml</import>

From 2173b85f99d755b77363077f47cd634426620251 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 13:35:29 +0200
Subject: [PATCH 63/97] corrected if statement for optional file

---
 tools/chewbbaca/AlleleCall.xml          | 4 ++--
 tools/chewbbaca/AlleleCallEvaluator.xml | 2 +-
 tools/chewbbaca/CreateSchema.xml        | 4 ++--
 tools/chewbbaca/ExtractCgMLST.xml       | 2 +-
 tools/chewbbaca/PrepExternalSchema.xml  | 4 ++--
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index b6a2296d7c6..50ff320d51b 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -12,13 +12,13 @@
         #end for
         unzip $input_schema -d 'schema' &&
         chewBBACA.py AlleleCall
-            #if str($training_file) != 'None'
+            #if $training_file:
                 --ptf $training_file
             #end if
             #if str($cds_input) != 'None'
                 --cds '$cds_input'
             #end if
-            #if str($genes_list) != 'None'
+            #if $genes_list:
                 --gl $genes_list
             #end if
             #if str($blast_score_ratio) != ""
diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 9fe21050d20..0303c5512d4 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -12,7 +12,7 @@
         #end for
         unzip $input_schema -d './schema' &&
         chewBBACA.py AlleleCallEvaluator
-            #if str($annotations) != 'None'
+            #if $annotations:
                 -a $annotations
             #end if
             $light
diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index d2995b2b70d..6f52b5cb596 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -10,10 +10,10 @@
         ln -sf $file './input/${file.element_identifier}' &&
         #end for
         chewBBACA.py CreateSchema 
-            #if str($training_file) != 'None'
+            #if $training_file:
                 --ptf '$training_file'
             #end if
-            #if str($cds_input) != 'None'
+            #if $cds_input:
                 --cds '$cds_input'
             #end if
             @INPUT@
diff --git a/tools/chewbbaca/ExtractCgMLST.xml b/tools/chewbbaca/ExtractCgMLST.xml
index 12ca89987a7..6194cb72751 100644
--- a/tools/chewbbaca/ExtractCgMLST.xml
+++ b/tools/chewbbaca/ExtractCgMLST.xml
@@ -14,7 +14,7 @@
         #if str($genes2remove) != 'false'
             --r './input/paralogous_counts.tsv'
         #end if 
-        #if str($genomes2remove) != 'None'
+        #if $genomes2remove:
             --g $genomes2remove
         #end if 
         -i 'input/results_alleles.tsv' -o 'output'
diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index 7fb47b81b7e..a7a92c48be7 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -8,10 +8,10 @@
         mkdir './schema' &&
         unzip '$input_schema' -d './schema' &&
         chewBBACA.py PrepExternalSchema
-            #if str($training_file) != 'None'
+            #if $training_file:
                 --ptf '$training_file'
             #end if
-            #if str($genes_list) != 'None'
+            #if $genes_list:
                 --gl '$genes_list'
             #end if    
             @INPUT@

From e50e9c63fd366b21a2db033e78285f788bfd243f Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 13:53:52 +0200
Subject: [PATCH 64/97] change some params to multiple select type

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 32 +++++++++++++++++--------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 0303c5512d4..919f35c5e4c 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -15,11 +15,21 @@
             #if $annotations:
                 -a $annotations
             #end if
-            $light
-            $no_pa
-            $no_dm
-            $no_tree
-            $cg_alignment
+            #if 'light' in $computation:
+                --light
+            #end if
+            #if 'no-pa' in $computation:
+                --no-pa
+            #end if
+            #if 'no-dm' in $computation:
+                --no-dm
+            #end if
+            #if 'no-tree' in $computation:
+                --no-tree
+            #end if
+            #if 'cg-alignment' in $computation:
+                --cg-alignment
+            #end if
             -i './input' -g './schema/schema_seed/' -o '${allelecall_report.files_path}' &&
         cp '${allelecall_report.files_path}/allelecall_report.html' '$allelecall_report'
     ]]></command>
@@ -28,11 +38,13 @@
         <param name="input_schema" format="zip" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
         <section name="advanced" title="Advanced options">
             <param argument="--annotations" type="data" format="tabular" label="Annotation file" help="File created by the UniprotFinder module" optional="true" />
-            <param argument="--light" type="boolean" truevalue="--light" falsevalue="" checked="false" label="Do not compute the presence-absence matrix, the distance matrix,  and the Neighbor-Joining tree." />
-            <param argument="--no-pa" type="boolean" truevalue="--no-pa " falsevalue="" checked="false" label="Do not compute the presence-absence matrix" />
-            <param argument="--no-dm" type="boolean" truevalue="--no-dm " falsevalue="" checked="false" label="Do not compute the distance matrix" />
-            <param argument="--no-tree" type="boolean" truevalue="--no-tree " falsevalue="" checked="false" label="Do not compute the Neighbor-Joining tree" />
-            <param argument="--cg-alignment" type="boolean" truevalue="--cg-alignment " falsevalue="" checked="false" label="Compute the MSA of the core genome loci, even if `--no-tree` is provided" />
+            <param name="computation" type="select" multiple="true" optional="true" display="checkboxes" label="Computation method">
+                <option value="light">Do not compute the presence-absence matrix, the distance matrix,  and the Neighbor-Joining tree. --light</option>
+                <option value="no-pa">Do not compute the presence-absence matrix. --no-pa</option>
+                <option value="no-dm">Do not compute the distance matrix. --no-dm</option>
+                <option value="no-tree">Do not compute the Neighbor-Joining tree. --no-tree</option>
+                <option value="cg-alignment">Compute the MSA of the core genome loci, even if `--no-tree` is provided. --cg-alignment</option>
+            </param>
         </section>
     </inputs>
     <outputs>

From 4718a0d467ae7cd8760ea240d7dabe6d99395e86 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 14:19:14 +0200
Subject: [PATCH 65/97] added '' to all files and directories

---
 tools/chewbbaca/AlleleCall.xml          |  8 ++++----
 tools/chewbbaca/AlleleCallEvaluator.xml | 12 ++++++------
 tools/chewbbaca/CreateSchema.xml        | 10 +++++-----
 tools/chewbbaca/DownloadSchema.xml      |  4 ++--
 tools/chewbbaca/ExtractCgMLST.xml       |  8 ++++----
 tools/chewbbaca/JoinProfiles.xml        |  2 +-
 tools/chewbbaca/NSStats.xml             |  2 +-
 7 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 50ff320d51b..aec9beedeb8 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -8,18 +8,18 @@
         mkdir 'input' &&
         mkdir 'schema' &&
         #for $file in $input_file
-        ln -sf $file 'input/${file.element_identifier}' &&
+        ln -sf '$file' 'input/${file.element_identifier}' &&
         #end for
-        unzip $input_schema -d 'schema' &&
+        unzip '$input_schema' -d 'schema' &&
         chewBBACA.py AlleleCall
             #if $training_file:
-                --ptf $training_file
+                --ptf '$training_file'
             #end if
             #if str($cds_input) != 'None'
                 --cds '$cds_input'
             #end if
             #if $genes_list:
-                --gl $genes_list
+                --gl '$genes_list'
             #end if
             #if str($blast_score_ratio) != ""
                 --bsr $blast_score_ratio
diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 919f35c5e4c..f51e05ae4b2 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -5,15 +5,15 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir './input' &&
-        mkdir './schema' &&
+        mkdir 'input' &&
+        mkdir 'schema' &&
         #for $file in $input_file
-        ln -sf $file './input/${file.element_identifier}' &&
+        ln -sf '$file' 'input/${file.element_identifier}' &&
         #end for
-        unzip $input_schema -d './schema' &&
+        unzip '$input_schema' -d 'schema' &&
         chewBBACA.py AlleleCallEvaluator
             #if $annotations:
-                -a $annotations
+                -a '$annotations'
             #end if
             #if 'light' in $computation:
                 --light
@@ -30,7 +30,7 @@
             #if 'cg-alignment' in $computation:
                 --cg-alignment
             #end if
-            -i './input' -g './schema/schema_seed/' -o '${allelecall_report.files_path}' &&
+            -i 'input' -g 'schema/schema_seed/' -o '${allelecall_report.files_path}' &&
         cp '${allelecall_report.files_path}/allelecall_report.html' '$allelecall_report'
     ]]></command>
     <inputs>
diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 6f52b5cb596..614520194b6 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -5,9 +5,9 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir './input' &&
+        mkdir 'input' &&
         #for $file in $input_file
-        ln -sf $file './input/${file.element_identifier}' &&
+        ln -sf '$file' 'input/${file.element_identifier}' &&
         #end for
         chewBBACA.py CreateSchema 
             #if $training_file:
@@ -18,9 +18,9 @@
             #end if
             @INPUT@
             --pm $prodigal_mode
-            -i './input' -o './output' &&
-        cd output/ &&
-        zip -r schema_seed.zip './schema_seed'
+            -i 'input' -o 'output' &&
+        cd 'output/' &&
+        zip -r schema_seed.zip 'schema_seed'
     ]]></command>
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
index 7ac145d8296..eb1b1318978 100644
--- a/tools/chewbbaca/DownloadSchema.xml
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -8,10 +8,10 @@
         chewBBACA.py DownloadSchema
             -sp $species_id 
             -sc $schema_id
-            -o './output' &&
+            -o 'output' &&
         ## The output is named based on the species name. Rename it to schema_seed so it is compatible for other chewbbaca tools.
         mv output/* 'schema_seed' &&
-        zip -r schema_seed.zip './schema_seed'
+        zip -r schema_seed.zip 'schema_seed'
     ]]></command>
     <inputs>
         <param argument="--species-id" type="select" label="Species ID">
diff --git a/tools/chewbbaca/ExtractCgMLST.xml b/tools/chewbbaca/ExtractCgMLST.xml
index 6194cb72751..753859a6fe1 100644
--- a/tools/chewbbaca/ExtractCgMLST.xml
+++ b/tools/chewbbaca/ExtractCgMLST.xml
@@ -5,17 +5,17 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir './input' &&
+        mkdir 'input' &&
         #for $file in $input_file
-        ln -sf $file './input/${file.element_identifier}.tsv' &&
+        ln -sf '$file' 'input/${file.element_identifier}.tsv' &&
         #end for
         chewBBACA.py ExtractCgMLST
         --t $threshold
         #if str($genes2remove) != 'false'
-            --r './input/paralogous_counts.tsv'
+            --r 'input/paralogous_counts.tsv'
         #end if 
         #if $genomes2remove:
-            --g $genomes2remove
+            --g '$genomes2remove'
         #end if 
         -i 'input/results_alleles.tsv' -o 'output'
     ]]></command>
diff --git a/tools/chewbbaca/JoinProfiles.xml b/tools/chewbbaca/JoinProfiles.xml
index 7d11e8a606f..819d042bca1 100644
--- a/tools/chewbbaca/JoinProfiles.xml
+++ b/tools/chewbbaca/JoinProfiles.xml
@@ -7,7 +7,7 @@
     <command detect_errors="exit_code"><![CDATA[
         chewBBACA.py JoinProfiles
             -p ${str($input1).replace(',', ' ')}
-            -o JoinedProfile.tsv
+            -o 'JoinedProfile.tsv'
             $common
     ]]></command>
     <inputs>
diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index c452bc6a755..85bfd297e36 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -13,7 +13,7 @@
             #if $schema_id != ""
             --sc $schema_id
             #end if
-            > NSStats.txt
+            > 'NSStats.txt'
     ]]></command>
     <inputs>
         <param argument="--mode" type="select" label="Mode" optional="false">

From c6acc9c602ced07d427480157df302da7ee7d8a0 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 14:19:28 +0200
Subject: [PATCH 66/97] added '' to all files and directories

---
 tools/chewbbaca/PrepExternalSchema.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index a7a92c48be7..b18cc58c6b4 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -5,8 +5,8 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir './schema' &&
-        unzip '$input_schema' -d './schema' &&
+        mkdir 'schema' &&
+        unzip '$input_schema' -d 'schema' &&
         chewBBACA.py PrepExternalSchema
             #if $training_file:
                 --ptf '$training_file'
@@ -16,8 +16,8 @@
             #end if    
             @INPUT@
             $size_filter
-            -g './schema/schema_seed/' -o './schema_seed' &&
-        zip -r PExternalschema_seed.zip './schema_seed'
+            -g 'schema/schema_seed/' -o 'schema_seed' &&
+        zip -r PExternalschema_seed.zip 'schema_seed'
     ]]></command>
     <inputs>
         <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>

From 01170b2f6ed2f92572bb697482dfb020c3e4e64f Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 14:25:08 +0200
Subject: [PATCH 67/97] better name for macros tokens

---
 tools/chewbbaca/CreateSchema.xml       | 4 ++--
 tools/chewbbaca/PrepExternalSchema.xml | 4 ++--
 tools/chewbbaca/macros.xml             | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 614520194b6..0053d0786fe 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -16,7 +16,7 @@
             #if $cds_input:
                 --cds '$cds_input'
             #end if
-            @INPUT@
+            @COMMON_INPUT@
             --pm $prodigal_mode
             -i 'input' -o 'output' &&
         cd 'output/' &&
@@ -28,7 +28,7 @@
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
             <param argument="--cds-input" type="data" format="txt" label="CDS input" optional="true" />
             <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
-            <expand macro="param" />
+            <expand macro="common_param" />
             <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="&quot;single&quot; for finished genomes, reasonable quality draft genomes and big viruses. &quot;meta&quot; for metagenomes, low quality draft genomes, small viruses, and small plasmids">
                 <option value="single" selected="true">
                         single
diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index b18cc58c6b4..102c1fadc4f 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -14,7 +14,7 @@
             #if $genes_list:
                 --gl '$genes_list'
             #end if    
-            @INPUT@
+            @COMMON_INPUT@
             $size_filter
             -g 'schema/schema_seed/' -o 'schema_seed' &&
         zip -r PExternalschema_seed.zip 'schema_seed'
@@ -25,7 +25,7 @@
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
             <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
             <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
-            <expand macro="param" />
+            <expand macro="common_param" />
             <param argument="--size-filter" type="boolean" truevalue="--size-filter" falsevalue="" checked="false" label="Size filter" help="Apply the minimum length and size threshold values to filter out alleles during schema adaptation" />
         </section>
     </inputs>
diff --git a/tools/chewbbaca/macros.xml b/tools/chewbbaca/macros.xml
index c4dd07ad70f..29c03430ea6 100644
--- a/tools/chewbbaca/macros.xml
+++ b/tools/chewbbaca/macros.xml
@@ -34,13 +34,13 @@
         <option value="15">Klebsiella oxytoca</option>
         <option value="16">Clostridium neonatale</option>
     </xml>
-    <token name="@INPUT@">
+    <token name="@COMMON_INPUT@">
         --bsr $blast_score_ratio
         --l $minimum_length
         --t $translation_table
         --st $size_threshold
     </token>
-    <xml name="param">
+    <xml name="common_param">
         <param argument="--blast_score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
         <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
         <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>

From 855121f7113eacab0fbc566549b76d0a8d4b1a5c Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 15:01:28 +0200
Subject: [PATCH 68/97] the result of AlleleCallEvluator is now a collection

---
 tools/chewbbaca/AlleleCallEvaluator.xml    | 45 +++++++++++-----------
 tools/chewbbaca/test-data/cgMLST_MSA.fasta |  2 +
 2 files changed, 24 insertions(+), 23 deletions(-)
 create mode 100644 tools/chewbbaca/test-data/cgMLST_MSA.fasta

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index f51e05ae4b2..92bcc0866af 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -8,7 +8,7 @@
         mkdir 'input' &&
         mkdir 'schema' &&
         #for $file in $input_file
-        ln -sf '$file' 'input/${file.element_identifier}' &&
+        ln -sf '$file' 'input/${file.element_identifier}.tsv' &&
         #end for
         unzip '$input_schema' -d 'schema' &&
         chewBBACA.py AlleleCallEvaluator
@@ -30,8 +30,7 @@
             #if 'cg-alignment' in $computation:
                 --cg-alignment
             #end if
-            -i 'input' -g 'schema/schema_seed/' -o '${allelecall_report.files_path}' &&
-        cp '${allelecall_report.files_path}/allelecall_report.html' '$allelecall_report'
+            -i 'input' -g 'schema/schema_seed/' -o 'output'
     ]]></command>
     <inputs>
         <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
@@ -48,33 +47,33 @@
         </section>
     </inputs>
     <outputs>
-        <data format="html" name="allelecall_report" label="${tool.name} on ${on_string}: AlleleCall Report"/>
+        <collection name="output_collection" type="list" format="tsv,fasta,js,html" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="__name_and_ext__" directory="output"/>
+        </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_exit_code="0">
             <param name="input_file">
                 <collection type="list">
-                    <element name="cds_coordinates.tsv" value="cds_coordinates.tsv" ftype="tabular"/>
-                    <element name="loci_summary_stats.tsv" value="loci_summary_stats.tsv" ftype="tabular"/>
-                    <element name="results_alleles.tsv" value="results_alleles.tsv" ftype="tabular"/>
-                    <element name="results_statistics.tsv" value="results_statistics.tsv" ftype="tabular"/>
+                    <element name="cds_coordinates" value="cds_coordinates.tsv" ftype="tabular"/>
+                    <element name="loci_summary_stats" value="loci_summary_stats.tsv" ftype="tabular"/>
+                    <element name="results_alleles" value="results_alleles.tsv" ftype="tabular"/>
+                    <element name="results_statistics" value="results_statistics.tsv" ftype="tabular"/>
                 </collection>
             </param>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
-            <output name="allelecall_report" file="allelecall_report.html" compare="sim_size"/>
-        </test>
-        <test>
-            <param name="input_file">
-                <collection type="list">
-                    <element name="cds_coordinates.tsv" value="cds_coordinates.tsv" ftype="tabular"/>
-                    <element name="loci_summary_stats.tsv" value="loci_summary_stats.tsv" ftype="tabular"/>
-                    <element name="results_alleles.tsv" value="results_alleles.tsv" ftype="tabular"/>
-                    <element name="results_statistics.tsv" value="results_statistics.tsv" ftype="tabular"/>
-                </collection>
-            </param>
-            <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
-            <param name="annotations" value="schema_seed_annotations.tsv"/>
-            <output name="allelecall_report" file="allelecall_report_annot.html" compare="sim_size"/>
+            <output_collection name="output_collection" type="list">
+                <element name="allelecall_report" file="allelecall_report.html">
+                    <assert_contents>
+                        <has_text_matching expression="report_bundle.js"/>
+                    </assert_contents>
+                </element>
+                <element name="cgMLST_MSA" file="cgMLST_MSA.fasta">
+                    <assert_contents>
+                        <has_text_matching expression="GCA_000007265"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
     </tests>
     <help>
diff --git a/tools/chewbbaca/test-data/cgMLST_MSA.fasta b/tools/chewbbaca/test-data/cgMLST_MSA.fasta
new file mode 100644
index 00000000000..cb1a4d92330
--- /dev/null
+++ b/tools/chewbbaca/test-data/cgMLST_MSA.fasta
@@ -0,0 +1,2 @@
+>GCA_000007265
+MVQYNNNYPQDNKEEAMTENEQLFWNRVLELSRSQIAPAAYEFFVLEARLLKIEHQTAVITLDNIEMKKLFWEQNLGPVILTAGFEIFNAEITANYVSNDLHLQETSFSNYQQSSNEVNTLPIRKIDSNLKEKYTFANFVQGDENRWAVSASIAVADSPGTTYNPLFIWGGPGLGKTHLLNAIGNQVLRDNPNARVLYITAENFINEFVSHIRLDSMEELKEKFRNLDLLLIDDIQSLAKKTLGGTQEEFFNTFNALHTNDKQIVLTSDRNPNQLNDLEERLVTRFSWGLPVNITPPDFETRVAILTNKIQEYPYDFPQDTIEYLAGEFDSNVRELEGALKNISLVADFKHAKTITVDIAAEAIRARKNDGPIVTVIPIEEIQIQVGKFYGVTVKEIKATKRTQDIVLARQVAMYLAREMTDNSLPKIGKEFGGRDHSTVLHAYNKIKNMVAQDDNLRIEIETIKNKIRMRYSKEIIQLAIPAMIENILQMLMGVVDNYLVAQLGVVAVSGVSVANNIITIYQAIFIALGASIASLLAKSLAGSKKDDAISVCSQAIFLTLLIGAVLGIISIVFGQTFFKLLGTTKSVAQVGGLYLAIVGGGVVTLGMLTTLGSFLRVQGQPRLPMYVSIFVNFLNAVLSGFAIFEWRYGLVGVAVSTLIARLIGICILAKYLPIKKIIKRMTWKISAQIWNLALPSAGERLMMRAGDVVIVAIVVQLGTNVVAGNAIGETLTQFNYMPGLGIATATIILTAKYVGQKNRESIEETIQSSYYIGLVLMILISSFMLLAGKPLTQLFTNNPSAIKGSLIVILLSFVGVPATIGTLVYTAAWQGLGNAKLPFYTTTIGMWLIRVVLGYLLGIVFELGLLGVWMATIADNIFRWLFLKVHYHRYIQKMMLVPKRVKHRREFRGKMRGEAKGGKEVSFGEYGLQATTSHWITNRQIEAARIAMTRYMKRGGKVWIKIFPHKSYTAKAIGVRMGSGKGAPEGWVAPVKRGKVMFEIAGVSEEVAREALRLASHKLPVKCKFVKREAEMGQKVHPIGMRVGIIRDWDAKWYAEKEYADYLHEDLAIRKFINKELADASVSTIEIERAVNKVIVSLHTAKPGMVIGKGGANVDALRGQLNKLTGKQVHINIIEIKQPDLDAHLVGENIARQLEQRVAFRRAQKQAIQRTMRAGAKGIKTQVSGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGEVLPARKNTKGGKMAEITSAKAMARTVRVSPRKTRLVLDLIRGKNVADAIAILKFTPNKAARVIEKTLNSAIANAENNFGLEKANLVVSETFANEGPTMKRFRPRAKGSASPINKRTTHVTVVVSEKMGRSLKKGPFVDEHLMKKVEAQANDEKKKVIKTWSRRSTIFPSFIGYTIAVYDGRKHVPVYIQEDMVGHKLGEFAPTRTYKGHAADDKKTRRMGIKVYKPTTNGRRNMTSLDFAEITTNTPEKSLLVSLKNKAGRNNNGRITVRHQGGGHKRHYRLIDFKRNKDGVEAVVKTIEYDPNRTANIALVHYTDGVKAYILAPKGLEVGQRIISGPEADIKVGNALPLANIPVGTVIHNIELQPGKGAELIRAAGASAQVLGQEGKYVLVRLQSGEVRMILGTCRATIGTVGNEQQSLVNIGKAGRNRWKGVRPTVRGSVMNPNDHPHGGGEGKAPVGRKAPSTPWGKPALGLKTRNKKAKSDKLIVRRRNQKMNLYDVIKKPVITEKSMVALEAGKYTFEVDTRAHKLLIKQAVEAAFDGVKVASVNTVTVKPKAKRVGRYTGFTSKTKKAIITLTADSKAIELFAAEAEMANVKLFDQTGKEVSSVELNEAIFGIEPNESVVFDVVISQRASLRQGTHAVKNRSAVSGGGRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYGYKLPQKVRRLALKSVYSAKVAEDKFVAVENLSFAAPKTAEFASVLSALSIDSKVLVILEEGNEFAALSARNLPNVTVATATTASVLDIVNADKLLVTKEAISTIEGVLAMTKGILGKKVGMTQIFTESGEFIPVTVIEATPNVVLQVKTVETDGYEAVQVGFDDKREVLSNKPAKGHVAKANTAPKRFIREFKNIEGLEVGAELSVEQFEAGDVVDVTGTSKGKGFQGVIKRHGQSRGPMAHGSRYHRRPGSMGPVAPNRVFKNKRLAGRMGGNRVTVQNLEIVQVIPEKNVVLIKGNVPGAKKSLITIKSAVKAAKMALTAGIVGLPNVGKSTLFNAITKAGAEAANYPFATIDPNVGMVEVPDERLQKLTELITPKKTVPTTFEFTDIAGIVKGASKGEGLGNKFLANIREVDAIVHVVRAFDDENVMREQGREDAFVDPIADIDTINLELILADLESINKRYARVEKMARTQKDKESVAEFNVLQKIKPVLEDGKSARTIEFTEEEAKVVKGLFLLTTKPVLYVANVDEDKVADPDDIDYVNQIRAFAETENAEVVVISARAEEEISELDDEDKLEFLEAIGLTESGVDKLTRAAYHLLGLGTYFTAGEKEVRAWTFKRGIKAPQAASIIHSDFERGFIRAVTMSYDDLIQYGSEKAVKEAGRLREEGKEYIVQDGDIMEFRFNVMANKKIRIRLKAYEHRTLDTAAEKIVETATRTGATVAGPVPLPTERSLYTIIRATHKYKDSREQFEMRTHKRLVDIINPTQKTVDALMKLDLPSGVNVEIKLMAIVYQSTRDASNKVTASQAILKGLADDGGLFTPITFPKVDLDFTKLKDASYQEVAKLVLSAFFDDFTEQELDYCISQAYDTKFDTTEIAPIVKIGDRYHLELFHGPTIAFKDMALSILPYLLTTAAKKQGVDNKIVILTATSGDTGKAAMAGFADVPGTEIIVFYPKNGVSYIQELQMITQAGQNTHVVAIEGNFDDAQTSVKEMFNNSLLRLKLSQQHMQLSSANSMNIGRLVPQIVYYIYAYAQLVKSKEISIGQPINFSVPTGNFGNILAAYYASQIGLPVTKLICASNDNNVLTDFFKTQTYDKNREFKVTSSPSMDILVSSNLERLIFHLLGDDAETTKKLMEDLVTTGEYALEARQANILESFVAGFATEQFVELDIKHLFDQYQYIEDPHTAVASAVYQAYQTETKDQTPAVIVSTASPYKFPCVVTKAITNKEEIQDFAAISILNDLSGVSLPKAVTDLQKAEVIHRTVVPTSNMRETVEECLGLKQMERNQRKTLYGRVVSDKMDKTITVVVETKRNHPVYGKRINYSKKYKAHDENNVAKEGDIVRIMETRPLSATKRFRLVEVVEKAVIIMKAVVVNQASTGVEVVEHDLPKVGHGEALVKVEYCGVCHTDLHVAHGDFGQVPGRILGHEGIGIVEEIGEGVTSLRVGDRVSIAWFFEGCGHCEYCTTGRETLCRSVKNAGYSVDGGMSEYAIVTADYAVKVPEGLDPAQASSITCAGVTTYKAIKEAGAAPGQWIAVYGAGGLGNLAVQYAKKVFNAHVVAVDINADKLQLAKEVGADLTVNGKEIKDVAAYIQEKTGGCHGVVVTAVSKVAFNQAIDSVRAGGTVVAVGLPSEYMELSIVKTVLDGIRVVGSLVGTRKDLEEAFAFGAEGLVVPVVEKVPVDTAPQVFDEMERGLIQGRKVLDFTKMTEKTKAVETTDVALAIDTLVQNGLKALDEMRQLNQEQVDYIVAKASVAALDAHGELALHAVEETGRGVFEDKATKNLFACEHVVNNMRHTKTVGVIEEDDVTGLTLIAEPVGVVCGITPTTNPTSTAIFKSLISLKTRNPIIFAFHPSAQESSAHAARIVRDAAIAAGAPENCVQWIEQPSIDATNALMNHDGIATILATGGNAMVKAAYSCGKPALGVGAGNVPAYVEKSANIRQAAHDIVMSKSFDNGMVCASEQAVIIDKEIYKEFVEEFKSYHTYFVNKKEKALLEEFCFGAKANSKNCAGAKLNPNIVGKSAVWIAEQAGFTVPEGTNILAAECTEVSEKEPLTREKLSPVIAVLKAESTEDGVEKARQMVEFNGLGHSAAIHTKDADLAREFGTRIRAIRVIWNSPSTFGGIGDVYNAFLPSLTLGCGSYGRNSVGDNVSAINLLNIKKVGRRRNNMQWFKVPSKTYFERDSIQYLQKCRDVERVMIVTDHAMVELGFLDRIIEQLDLRRNKVVYQIFAEVEPDPDITTVMKGTDLMRTFKPDTIIALGGGSPMDAAKVMWLFYEQPEVDFHDLVQKFMDIRKRAFKFPELGKKTKFVAIPTTSGTGSEVTPFAVISDKANNRKYPIADYSLTPTVAIVDPALVMTVPGFIAADTGMDVLTHATEAYVSQMANDYTDGLALQAIKIVFDYLERSVKDADFEAREKMHNASTMAGMAFANAFLGISHSMAHKIGAQFHTVHGRTNAILLPYVIRYNGTRPAKTATWPKYNYYRADEKYQDIAKLLGLPAATPEEAVESYAKAVYDLGTRLGIKMNFRDQGIDEKEWKEKSRELAFLAYEDQCSPANPRLPMVDHMQEIIEDAYYGYEERPGRRKMRIKWFSLVRITGLLLVLLYHFFKNSFPGGFVGVDIFFTFSGFLITALLIDEFSKTKKIDFVSFCRRRFYRIFPPLVLMVLVTIPFVFLVKSDFRASIGSQIMTALGFTSNFYEILTGGNYESQFIPHLFVHTWSLSIEVHFYVLWGLTVWLLSKRSKDQKQLRGTLFLISMGIFGVSFLTMFVRAFFVDNFSTIYFSTLSHIFPFFLGAMVATISGIREITGRFKKNIKNLTLKHNLIMMGSAFAGLMILTFALDFDNRLTYLFGFVLSSIFASVMIYNARILHEHTPDISEPFVITYLADISYGMYLFHWPFYIIFSRLSPNWIAVILTVVLSAVFSTLSFYIIEPFILGRKPKFLDYEFDLLPYKKWLFSIGGVLTLITVVTMLTAPSIGSFETELLQNSLQQARTNTNRTHTLAAGDAGALSDVTVIGDSVALRSSAAFNKLLPEVQLDAAVSRNFSKSFDIFENRIQNKALSKIVVLAVGVNSLDNYKTDLSQFIKSLPKGHRLIIVTPYNAKNMSQVTTVRDYELSLMKKYNYITVADWYKVATEHPEIWGNTDGVHYSDSDTTGADLYVSNVKKAIQKSAQRAAKMKNFKITRTHLEILSLIIIVVFGLSVFTLTTSSQGVFSYDGGKIKYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHGWSYTGDFKKGQPDGQGRLNAKNKKVYKGTFKQGIYQKMKKVCFVCLGNICRSPMAEFVMANLDKEDSLLVESRATSTWEHGNPIHRGTQAILQRYQIPYINDKGSQPISKDDLAYFDYIIGMDEQNVKDLKALSQGTYDDKISLFCDGGVPDPWYTGDFEETYRLVNDGCKQWLTLINNSRDMTRFLDSDAMGDEELVERTLRPQYLREYIGQDKVKDQLKIFIEAAKLRDESLDHVLLFGPPGLGKTTMAFVIANELGVNLKQTSGPAIEKSGDLVAILNDLEPGDVLFIDEIHRMPMAVEEVLYSAMEDFYIDIMIGAGETSRSVHLDLPPFTLIGATTRAGMLSNPLRARFGITGHMEYYEENDLTEIIERTADIFEMKITYEAASELARRSRGTPRIANRLLKRVRDYAQIMGDGLIDDNITDKALTMLDVDHEGLDYVDQKILRTMIEMYNGGPVGLGTLSVNIAEERDTVEDMYEPYLIQKGFIMRTRTGRVATVKAYEHLGYQRFDKMLKHFGSKVRNLRVTRNITREDFCGDETELSVRQLARIESGQSIPNLTKAHYIAKQLNVKLDILTGGESLELPKRYKELKYLILRIPTYADAERLKLRECQFDHIFEEFYDNLPEDECLAIDSLQAKFEVYQTGDINFGVEVLCECFDKVKYKEKYTLNDLIIIDLFLTCAVVSKFNNRAFTKEVFQTICKTLISQNHKLTAEDLFWFNHVLLNCVFVGLCLNSEECLAEMLEVSRQTMVSTHDFHKMPLYFMYQWKYFITIDNDIKSAENAYQQSIMFSKMIDDKHLIKKLELEWQEDITGHMDNLIRLAEIFDVSLDEHVLAKTNEVKVERIYENKPLDLRKYNKIYWFIFRNIIRSLLIILAILTFLMIERYSRPEMAAIWTEENKYRAWLEVEILADEAWAELGEIPKEDVAKIREKADFDIDRILEIEQDTRHDVVAFTRAVSETLGEERKWVHYGLTSTDVVDTAYGYLYKQANDIIRRDLENFTNIVADKAKEHKFTIMMGRTHGVHAEPTTFGLKLATWYSEMKRNIERFEHAAAGVEAGKISGAVGNFANIPPFVEQYVCDKLGIRPQEISTQVLPRDLHAEYFAVLASIATSIERMATEIRGLQKSEQREVEEFFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGHMVTAYENVALWHERDISHSSAERIITPDTTILIDYMLNRFGNIVKNLTVFPENMMRNMESTFGLIYSQRVMLKLIEKGMTREEAYDLVQPKTAYSWDNQVDFKPLLEEDTKVTSCLTQEEIDELFNPIYYTKRVDDIFERLGLEKMNRIINRDILPRISKISKNNKEKDLLSIAYITWLIFIIFALGVVTVNDLKPMFNQLIVNLLNIYYYMEAFILGMDSYLQYNLPYSFDFWSIFVEAINLFVKVFLIAFIPSVIRKVLKKESFFNEVVILLGAIVTIIVSFHLYLEILIVVGLILLLIAFVSIGKNRVYNFVQNLNYFEEVIWNYFEENPVKIKEKSLIIKFLLTISFVFVIDFAMVRLLNFNIKFSTILACSAILLAWLYQNKSVTEPFLLKKLVIYFIFFIATLIGNLKNELSILETPLLFISIFFTMDRIIALSKEMRDLIISKSILFYYDHENIKPSILLSEIKEIKYLENVDIGELELVRQMVIRLRLELEEEFLILSDIYMKNGYEKYIQFVQGNVYFINLELDKIPNYTNLKLILESIFDHNNQKIFIPKLYEEYIYILISLGEVEKAKEILKEVSDYLTEESLNYFEKEYDKAKGSNMKLQEIKDFVKELRGLSQEELAKKENELKKELFDLRFQAAAGQLEKTARLDEVKKQIARVKTVQSEMKMVKMIVGLGNPGSKYNDTKHNIGFMAVDRIVKDLDVNFTEDKNFKAEIGSDFINGEKIYFIKPTTFMNNSGIAVKALLTYYNISIKDMIIIYDDLDMEVGKIRFRQKGSAGGHNGIKSIIAHLGTQEFDRIKVGIGRPNGRMTVINHVLGKFDKNDEIMILNTLDKVDNAVNYYLQTNDFQKTMQKYNGLKMSKPNVVQLNNQYINDENLKKRYEAEELRRKNRLMGWVLIFVMLLFILPTYNLVKSYRTLQERRQEVVKLTKDYQTLTNRTENQKLLAKQLKNPDYVQKYARAKYYFSKTGEMIYPLPDLLPKMARIAGVDIPNDKRVVISLTYVYGIGLSTSKKILAAAGISEDIRVKDLTPDQEDAIRREVDAIKVEGDLRREVNLNIKRLMEIGSYRGIRHRRGLPVRGQNTKNNARTRKGKAVAIAGKKKMKKNKIIRFSLVGVLLAILCFSLFALLKPNSQQSSSQKLRNEDIKKISSQKRNKKLQLPAVSSKDWNLILVNRDHKHEELSPDVVPVENIYLDKRITKQATQFLEAARAIDSREHLISGYRSVAYQEKLFNSYVTQEMTSNPNLTRGQAEKLVKTYSQPAGASEHQTGLAMDMSTVDSLNESDPRVVSQLKKIAPQYGFVLRFPDGKTAETGVGYEDWHYRYVGVESAKYMAKHHLTLEEYITLLKENNQMSKVRLYIARHGKTMFNTIGRAQGWSDTPLTTFGELGIKELGLGLKASNISFKEAFSSDSGRTLQTMEIILREVQQENIPYTRDKRIREWCFGSLDGGYDGDLFNGVLPRVSNGDMSHLTHEEIANLICQVDTAGWAEPWAILSNRILSGFTAIAKKIEDIGGGNAIVVSHGMTIATFLWLIDHSTPRSLGLDNGSVSVVDFEDGTFSIQSIGDMSYREKGREILEKTLQMRDFEELFDKVKPIVMKLRRNYFVQLWEYDDWIQEGRIVLFRLLEEHPYLLDNESKLFIYFKTKFSNYLNDVLRHQDCQKRQFNKMPYEEISEVSHYVKSKGLVLDDYIAYRDTLTKVEETLSDIDKEKFEKLISGERFAGKKQFIRDIQPFFNAFKADMKMTVYFDGNFWLGLIEYDDDGDYKVFRYFFGKEPKDDDVFNFINHKLNDLIKKYEFVKTDISLKRTNEHKKSPKRMQREINREKRKPVVSTKAQLAMKTIHMSIKNERQLSQKCKKNELRKHRYQLKQEKRYQKKKGHMTKIYHMILCNSDIMKILAIIKSLPLNDCWLCAGTLRNFVWNKLSGINETLTSDIDVVFFDKNISYEETVVLEQQLKDNYPQYDWELKNEFYMNTHSPNTPKYTSSKDAISKFPEKCTAVGARLDDRNQLELYLPYGEEEILNFIVSPTPYFEEDLLRYNVYLKRVDKKKWNNIWPRLTIIKKMINKPLLRKNKNNNIVIPPNTSNKLTFSSLKISSLFHMYKVIKRILKTMYQYMTLDTRLKYFNFYSPFKDVFENTIMEHTYSKILNMRLDKYLKVSRIIKRRPVAKEVADKGRVKVNGVLAKSSTDLKLNDQVEIRFGNKLLTVKVLEMKDSTKKEDAIKMYEIINETRIETDEQAMAYRKLGRTSSQRKAMLRDLTTDLLINESIVTTEARAKEIRKTVEKMITLGKRGDLHARRQAAAYVRNEIASENYDEASDKYTSTTALQKLFDDIAPRYAERNGGYTRILKTEPRRGDAAPMAIIELVMIEFEKPIITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKIKLADLGLGLKNDKMAKPTRKRRVKKNIESGVAHIHATFNNTIVMITDVHGNALAWSSAGALGFKGSRKSTPFAAQMAAEAAAKSAQEHGLKTVEVTVKGPGSGRESAIRALAAAGLEVTAIRDVTPVPHNGARPPKRRRVMAKEDVIEIEGKVVETMPNAMFTVELENGHQILATVSGKIRKNYIRILVGDRVTVEMSPYDLTRGRITYRFKMIQQETRLKVADNSGAREILTIKVLGGSGRKFANIGDVIVASVKQATPGGAVKKGDVVKAVIVRTKTGARRPDGSYIKFDDNAAVIIRDDKTPRGTRIFGPVARELREGGYMKIVSLAPEVLMNLLIMGLPGAGKGTQAAKIVEEFGVAHISTGDMFRAAMANQTEMGRLAKSYIDKGELVPDEVTNGIVKERLAEDDIAEKGFLLDGYPRTIEQAHALDATLEELGLRLDGVINIKVDPSCLIERLSGRIINRKTGETFHKVFNPPVDYKEEDYYQREDDKPETVKRRLDVNIAQGEPILEHYRKLGLVTDIEGNQEITEVFADVEKALLELKMFLKLLRDALKVKMVRNKILFTIFILLVFRIGTHITVPGINVKSLEQMGELPFLNMLNLVSGNAMRNFSVFSMGVSPYITASIVVQLLQMDILPKFVEWGKQGEVGRRKLNQATRYISLFLAFVQSIGITAGFNTLSSVALVKTPNVQTYLLIGAILTTGSMVVTWLGEQITDKGFGNGVSMIIFAGIISSIPSAITTIYEDFFVNVRSSAITNSYIFVGILIVAVLAIVFFTTFIQQAEYKIPIQYTKLVQGAPTSSYLPLKVNPAGVIPVIFASSITTIPSTIIPFFQNGKEIPWLTKLQELLNYQTPVGMIIYAILIILFSFFYTFVQVNPEKTAENLQKNSSYIPSIRPGRETEEYMSSLLKKLATIGSVFLAFISLLPIIAQQALHLSSSIALGGTSLLILIATGIEGMKQLEGYLLKRRYVGFMNTTEMNIIELFSQNKVVRTWHSGLVTNSRQLVMGFSGASKAIAIASAYEKLSKKIMVVTATQTDSDKLSSDISSLIGEDNVYQFFADDVPAAEFIFSSLDKSISRLSALRFLKDPEKNGVLITSISGLRLLLPNPEVFSKSQYKFEIGQECYLDKLCKNLVNLGYQKVSQVFSPGEFSQRGDILDIFEMTQEYPYRLEFFGDEIDGIRQFDIDTQKSLKQLESVQISPADDIILQDADFERAKKKLEGYLVTASEVQRTYLSEVLSTTENHFKHSDIRRFLSIFYEKEWGILDYIPEGTPLFVDDFQKIVDRNAKLDLEIASLLTEDLQQGKSHSSLNYFSDPYKQLRQYQPATFFSNFHKGLGNLKFDKLHHFTQYGMQEFFNQFPLLVDEINRYKKSGATVLLQVDSQKGLNLLQENLKEYGLDLIISDKNDIVQKESQLIVGHLSNGFYFADEKIVLITEREIYHRRVKRKIRRSNISNAERLKDYNELSVGDYVVHNVHGVGKFLGIETIEIQGIHRDYLTIQYQNADRISIPVEQIELLTKYVSADGKEPKINTLNDGRFKKAKQRVAKQVEDIADDLLKLYAERSQLQGFAFSPDDNMQNDFDNDFAYVETEDQLRSIKEIKQDMEGNRPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVVVLVPTTVLAQQHFENFKERFSNYPVTVDVLSRFRSKKEQTDTLKRLSKGQVDIIIGTHRLLSQDVVFSDLGLIVIDEEQRFGVKHKEKLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLETNPGLVREAIIREIDRGGQVFYVYNKVDTIDQKVSELQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNTLFVENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEISEKRLDAIKGFTELGSGFKIAMRDLSIRGAGNILGASQSGFIDSVGFEMYSQLLEQAIATKQGKSLIRQKGNAELALQIDAYLPAEYISDERQKIEIYKRIRELETRADYEALQDELIDRFGEYPDQVAYLLEIGLLKAYLDLAFTELVERKGNEISILFEKASLKYFLTQDYFEALSKTQLKARISETNGKMEVVFNIKHKKNYEIIEELLKFAECFIEIKSRKPVEEMKLHELKPAEGSRKVRNRVGRGTSSGNGKTSGRGQKGQKARSGGGVRLGFEGGQTPLFRRMPKRGFSNINAKEYALVNLDQLNVFEDGTEVTPVVLKEAGIVRAEKSGVKILGNGELTKKLSVKAAKFSKSAEAAITAKGGSIEVIMAFKDNAVELEERVVAINRVTKVVKGGRRLRFAALVVVGDRNGRVGFGTGKAQEVPEAIRKAVEAAKKNMVEVPMVGTTIPHEVRSEFGGAKVLLKPAVEGAGVAAGGAVRAVIELAGVADITSKSLGSNTPINIVRATVEGLKQLKRAEEVAALRGISVSDLAMISKPDKNKIRQKRHRRVRGKLSGTADRPRLNIFRSNTGIYAQVIDDVAGVTLASASTLDKEVSNGTKTEQAVVVGKLVAERAVAKGISEVVFDRGGYLYHGRVKALADSARENGLKFMSRIGNKVITLPAGVEIINKDNVVTVKGPKGQLTREFNKNIGITVEGTEVTVTRPNDSKEMKTIHGTTRANLNNMVVGVSEGFKKALEMRGVGYRAQLQGSKLVLSVGKSHQDEVEAPEGVTFEVPTPTTINVIGINKESVGQTAAYVRSLRSPEPYKGKGIRYVGEFVRRKEGKTGKMVMTDPIADFLTRIRNANQAKHEVLEVPASNIKKGIADILKREGFVKNVEVIEDDKQGIIRVFLKYGQNGERVITNLKRISKPGLRVYTKHEDMPKVLNGLGIAIVSTSEGLLTDKEARQKNIGGEVLAYIWMANRLKEKYTNEVVPALTEKFNYSSVMAVPKVEKIVLNMGVGDAVSNAKNLEKAAAELALISGQKPLITKAKKSIAGFRLREGVAIGAKVTLRGERMYEFLDKLVSVSLPRVRDFHGVPTKSFDGRGNYTLGVKEQLIFPEINFDDVDKVRGLDIVIVTTANTDEESRELLKGLGMPFAKMFVKKGDKVRVIAGKDKGTEAVVLKALPKVNKVVVEGVALIKKHQKPNNENPQGAIVEKEAPIHVSNVQVLDKNGVAGRVGYKVVDGKKVRYNKKSGEVLDMNSFKTIGIIGGGQLGQMMAIAAIYMGHKVITLDPASDCPASRVSEVIVAPYDDVEALGTLAARCDVLTYEFENVDADGLDAVVSAGQLPQGTDLLRISQNRIFEKDFLANKAGVTVAPYKVVTSSLDLEGLDLTKTYVLKTATGGYDGHGQKVIRSAEDLPEAQQLANSAQCVLEEFVNFDLEISVIVSGNGQDVTVFPVQENIHRNNILSKTIVPARISDQLADKAKEMAVQIAKKLQLSGTLCVEMFATADDIIVNEIAPRPHNSGHYSIEACDFSQFDTHILGVLGAPLPPIKLHAPAVMFNVLGQHVQQAIDHVAQNPSAHLHMYGKLEAKHNRKMGHVTVFSDVPDEVEEFEERMDFMQKTAEVLDNFGIAYEKKVVSAHRTPDLMFKHAEEARGRGIKIIIAGAGGAAHLPGMVAAKTTLPVIGVPVKSRALSGLDSLYSIVQMPGGVPVATMAIGEAGATNAALTALRILSIEDQNLADALAHFHEEQGKIAEESSNELIMKLLVVGSGGREHAIAKKLLASKDVDQVFVAPGNDGMTLDGLDLVNIGISEHSRLIDFVKENEIAWTLIGPDDALAAGIVDGFNSAGLRAFGPTKAAAELEWSKDFAKEIMVKYNVPTAAYGTFSDFEKAKAYIEEQGAPIVVKADGLALGKGVVVAETVEQAVEAAQEMLLDNKFGDSGARVVIEEFLDGEEFSLFAFANGDKFYIMPTAQDHKRAYDGDKGLNTGGMGAYAPVPHLPQSVVDTAVETIVKPVLEGMIAEGRPYLGVLYAGLILTADGPKVIEFNSRFGDPETQIILPRLTSDFAQNIDDIMMGIEPYITWQKDGVTLGVVVASEGYPLDYEKGVPLPEKTDGDIITYYAGAKFAENSKALLSNGGRVYMLVTTEDSVKAGQDKIYTQLAQQDTTGLFYRNDIGSKAIKEMTIYDQIESALDLMTDLEREIACYFMGQPISKDALASTIVTKQLHISQAALTRFAKKCGFKGYREFVFEYLKSHETISQQLYGLQNDNTKKVFMNYQEMISKSADIIDEEQLLEVSHMIEQADRVYFYGKGSSSLVAKEFKIRLMRLGVICEALDDTDSFSWTNSIVNDRCLVIAFSLSGNTNSVIGALKIASCHGAKTVLFTKQPHTIDYAFDKIIQVASARHLDYGNRISPQIPMLIMVDIIYAQFLDINKIEKERIFRETIIQRMIHFSINKNFFLHALTVTKRAISHKNAIPILSTVKIEVTRDAIILTGSNGQISIENTIPASNENAGLLVTNPGSILLEAGFFINIISSLPDVTLEFTEIEQHQIVLTSGKSEITLKGKDVDQYPRLQEMTTDTPLTLETKLLKSIINETAFAASQQESRPILTGVHLVISQNKYFKAVATDSHRMSQRTFQLEKSANNFDLVVPSKSLREFSAVFTDDIETVEVFFSDSQMLFRSENISFYTRLLEGNYPDTDRLLTNQFETEIIFNTNALRHAMERAYLISNATQNGTVRLEIQNETVSAHVNSPEVGKVNEELDTVSLKGDSLNISFNPTYLIESLKAVKSETVTIRFISPVRPFTLTPGEDTEDFIQLITPVRTNMKKRILSAVLVSGVTLGTAAVTVNADDFDSKIAATDSVINTLSGQQAAAQNQVTAIKGQVGALESQQSELEAQNAQLEAVSQQLGQEIQTLSNKIVARNESLKKQVRSAQKGNLTNYINTILNSKSVSDAVNRVVAIREVVSANEKMLAQQEADKAALEAKQIENQNAINTVAANKQAIENNKAALATQRAQLEAAQLELSAQLTTVQNEKASLIQAKAQAEEAARKAAEAQAAAEAKAQAEAKAQAESVAKAQAAAQVESATAPTETVQTQPRTEIKPSNLTATSSATTVATTTATATNEPKVTQPSVVTKAVEAPKAVVSSTPRAVSKPVVRSYDSSNTYPMGQCTWGAKSMASWVGNYWGNANQWGASARAAGYSVGTTPRVGAVAVWPYDGGGYGHVAVVTSVANNSSIQVMESNYAGNMSIGNYRGSFNPSASGSVYYIYPNMKNNKNNGFLKNSFIYILLIIAVITTFQYYLKGTSSQNQQISYTKLVKQLKAGEIKSISYQPSGGVVEVSGTYKKAKTIKSANSFTFLGGSVATKVTGFNSVILPNDSSIKSLVSAAEENNTNIQVKHESSSGTWISYIASFLPLVIMIGFFMMMMNQGGGGGARGAMSFGKNKARSSSKDEVKVRFSDVAGAEEEKQELIEVVDFLKDPKRYKSLGARIPAGVLLEGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAERAIIFIDEIDAVGRRRGAGMGGGNDEREQTLNQLLIEMDGFEGNESIIVIAATNRSDVLDPALLRPGRFDRKVLVGQPDVKGREAILRVHAKNKPLADNVDLKVVAQQTPGFVGADLENVLNEAALVAARRNKKVIDASDIDEAEDRVIAGPSKKDRTISERERAMVAYHEAGHTIVGLILSNARVVHKVTIVPRGRAGGYMIALPKEDQMLLSKDDMKEQLAGLMGGRVAEEIIFNAQTTGASNDFEQATAMARAMVTEYGMSEKLGPVQYEGNHAMMAGQMSPEKSYSAQTAQLIDDEVRHLLNEARNKAADIINENRDTHKLIAEALLKYETLDAAQIKSIFETGKMPETENDEDKARALSYDEIKEKMQEEDKKMLENDIKKVLYSEEDIILKTKELGAKLTADYAGKNPLLVGVLKGSVPFMAELLKHIDTHVEIDFMVVSSYHGGTTSSGEVKILKDVDTNIEGRDVIFIEDIIDTGRTLKYLRDMFKYRQANSVKVATLFDKPEGRLVDIDADYVCYDIPNEFIVGFGLDYAENYRNLPYVGVLKEEIYSKMYNTILKDTLSKGLFTAHQKVLIAVSGGIDSINLLQFLYQYQKELSISIGIAHINHGQRKESEKEEEYIRQWGQIHDVPVFISYFQGIFSEDRARNHRYNFFSKVMREEGYTALVTAHHADDQAETVFMRILRGSRLRYLSGIKQVSAFANGQLIRPFLPYKKELLPNIFHFEDASNASSDYLRNRIRNVYFPALERENNQLKDSLITLSEETECLFTALTDLTRSIEVTNCYDFLRQTHSVQEFLLQDYISKFPDLQVSKEQFRVILKLIRTKANIDYTIKSGYFLHKDYESFHITKIHPKTDSFKVEKRLELHNIQIFSQYLFSYGKFISQADITIPIYDTSPIILRRRKEGDRIFLGNHTKKIRRLFIDEKITLKEREEAVIGEQNKELIFVIVAGRTYLRKPSEHDIMKGKLYIENLEKRMSKVRGFELVSQFSNKELLPKRETAHAAGYDLKVAKKTVIEPGEITLVPTGIKAYMQPGEVLYLYDRSSNPRKKGIVLINSVGVIDGDYYNNQVNEGHIFAQMQNITDQAVILEEGERIVQAVFAPFLLADDDQATGMRTGGFGSTGKMKKIRLSKFIKMIVVILFLISVAASFYFFHVAQVRDDKSFISNGQRKPGNSLYAYDKSFDKLLKQKIEMTNQNIKQVAWYVPAVKKTHKTAVVVHGFANSKENMKAYGWLFHKLGYNVLMPDNIAHGESHGQLIGYGWNDRENIIKWTEMIVDKNPSSQITLFGVSMGGATVMMASGEKLPSQVVNIIEDCGYSSVWDELKFQAKEMYGLPAFPLLYEVSTISKIRAGFSYGQASSVEQLKKNNLPALFIHGDKDNFVPTSMVYDNYKATAGKKELYIVKGAKHAKSFETEPEKYEKRISSFLKKYEKMTKYIFVTGGVVSSIGKGIVAASLGRLLKNRGLKVTIQKFDPYINIDPGTMSPYQHGEVYVTDDGAETDLDLGHYERFIDINLNKYSNVTTGKIYSEVLKKERRGEYLGATVQVIPHVTDALKEKIKRAATTTDSDVIITEVGGTVGDIESLPFLEALRQMKADVGSDNVMYIHTTLLPYLKAAGEMKTKPTQHSVKELRGLGIQPNMLVIRTEQPAGQSIKNKLAQFCDVAPEAVIESLDVDHIYQIPLNMQAQNMDQIVCDHLKLETPAADMTEWSAMVDKVMNLEKKVKIALVGKYVELPDAYLSVVEALKHSGYVNDVAIDLKWVNAAEVTEDNIKELVGDADGIIVPGGFGQRGSEGKIEAIRYARENDVPMLGVCLGMQLTCVEFARNVLNLHGANSAELDPKTPFPIIDIMRDQIDIEDMGGTLRLGLYPCKLKSGSRAAAAYNNQEVVQRRHRHRYEFNTKFREQFEAAGFVFSGVSPDNRLMEVVELPEKKFFVAAQYHPELQSRPNHAEELYTAFVTAAVENMKMELEVFAGQEKSELSMIEVARAILEQRGRDNEMYFSDLVNDIQTYLGKSDSAIRESLPFFYSDLNTDGSFIPLGENKWGLRSWYAIDEIDEEIITLEEDEDGAPKRKKKRVNAFMDGDEDAIDYNDDDPEDEDFTEETPSLEYDEENPDDEKSEVESYDSEINEIIPDEDLDEDVEINEEDDEEEEEEEEVMSTSFENKATNRGIITFTISQDEIKPALDQAFNKVKKDLNVPGFRKGHMPRTVFNQKFGEEALYENALNLVLPKAYEAAVAELGLDVVAQPKIDVVSMEKGQDWKLTAEVVTKPEVKLGDYKDLSVEVDASKEVSDEEVDAKVERERNNLAELTVKDGEAAQGDTVVIDFVGSVDGVEFDGGKGDNFSLELGSGQFIPGFEEQLVGSKAGQTVDVNVTFPEDYQAEDLAGKDAKFVTTIHEVKTKEVPALDDELAKDIDDEVETLDELKAKYRKELESAKEIAFDDAVEGAAIELAVANAEIVELPEEMVHDEVHRAMNEFMGNMQRQGISPEMYFQLTGTTEEDLHKQYQADADKRVKTNLVIEAIAAAEGFEATDEEIEKEITDLASEYNMEADQVRGLLSADMLKHDIAMKKAVDVITSSATVKMKKVLTFLLCSLYFVSIPAISTEEPLTLSQNRRYALTQTVVDKEMYFDAIPERPTTKIEISSFQDEALTITGETLVPNTLLSIVSLTINSNGIPVFTLSNGQFIKASREAIFNDLVSKQQSVSLDYWLKPSFVTYEAPYTNGVSEVKNNLKPYSRVHLVEQAETEHGIYYKTDSGFWISVEDLSVADNRMAKVQEVLLEKYNKDKYGIYIKQLNTQTVAGINIDRSMYSASIAKLATLYASQEQVKLGKLSLDSKFEYKDNVNQFPNSYDPSGSGKLEKKADHKLYTVKELLEATAKESDNVATNMLGYYVNNQYDSMFQTQVDTISGMHWDMKKRQISPQAAGKMMEAIYYQNGDIVNYLSKTDFDNTRIPKNIPVKVAHKIGDAYDYKHDAAIVYAEQPFIMIIFTDKSSYDDITKIADDVYQVLKMITLEKFIDHLNVEEVLFTFFTKLISILLLIIAFVIVRQVINYLFEKTVNRSLAFSRQKVARQKTLAKLSHNVLNYTLYFFLFYWILSILGVPISSLLAGAGIAGVAIGLGAQGFLSDVVNGFFILLENQFDVGDIINVGTVSGTVTNVGIRTTQIHDFDGTLHFIPNRNITIVSNKSRSNMRAQIDIPLFVHTNLDQISDIVTKINEEYVSKHPAIVGEPTVFGPTTNANGQFVYRINIFTQNGAQFDIYAEFYKLYQKAILEEGIDLPTYNFSNNHSRMILDYNKLKQETKAIVVDIIERSALKKGQIFVLGLSSSEVSGGLIGKNSSSEIGEIIVEVILKELHSRGIYLAVQGCEHVNRALVVEAELAERQQLEVVNVVPNLHAGGSGQVAAFKLMTSPVEVEEIVAHAGIDIGDTSIGMHIKRVQVPLIPISRELGGAHVTALASRPKLIGGARAGYTSDPIRKFMRKEKTSQLVQLAIVTAISIVLGMFISIPTPTGFLTLLDAGIFFAAFYFGKKEGAVVGALAGFLIDLLKGYPNWMFFSLLIHGTQGYLAGLPGRRRLLGLISATLVMVLGYAIASGLMYGWGAVLPDIPGNIMQNMVGMVVGFALNKSLERVKKMKTRNVLAISGNDIFSGGGLHADLATYVVNKLHGFVAVTCLTAMSDKGFEVIPIEASILKQQLESLKDVEFGSIKLGLLPNVETAQVVLEFVKSKQECPVVLDPVLVCKENHDLEVSQLREQLIAFFPYADVITPNLVEAQLLTGLSIENLDQMKIAAEKLYDMGAKHVVIKGGNRLNAEEATDLYYDGERFETYVFPVVDANNTGAGCTFASSIASQLAMGKNVEDAVKMSKGFVYQAIKASDKYGVVQHFMTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDVGVHAYGQVIHFDLPQARDVEKLRFGLDTQCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIGRPKNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQFEASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGNGLYLKEIIYEDEECFSNFRKMVTKVEEIRSYLIASIQNGKLAPGDRLPSIRQLANQFSCNKDTVQRVLMELRFDNYIYAKPRSGYYVFDSHQEEVEEGVSLPNSEIANIAYDDFRLCLNETLIGREDYLFNYYYRQEGLLDLSKAVAKLMEETGVYVPLDDIVITAGTQQALFILTQVTFPNRKSRVLIEEPTYPRMIELIKTQNLPYETISRGTHGIDFQRLEEIFQTQSIKFFYVIPRMHNPLGTSYNPVEMKRLIEMAEKYDVYIVEDDYMSDFASQSPLHYYDTHGRVIYLKSFSKAIFPALRLAAICLPQALKSTFMAYKKLMDYDTNLILQKALALYIENGLYAKNSQYLKYRYQKDLANSKSILADHPNLPSYSLHHDSVLFDCSKLDNFKILRQYGDTLENYFCQKSHQSLLQVKNDSCLKQFLGSLMNNTEFYDRLGVSKDASQDEIKKAYRRMSKKYHPDINKETGAEEKYKEVQEAYETLSDTQKRAAYDQYGAAGANGGFGGFDGGGFGGFDGGGFGGFEDIFSSFFGGGGMRNPNAPRQGDDLQYRVNLSFEEAIFGAEKEVSYNRESSCHTCSGSGAKPGTSPVTCQKCHGSGVINVDTQTPLGTMRRQVTCDVCQGSGQEIKEKCPTCHGTGHEKKTHKVSVKIPAGVETGQQIRLTGQGEAGFNGGPYGDLFVIINVLPSQQFERNGSTIYYTLNISFVQAALGDTIDIPTVHGAVEMSIPAGTQTGKTFRLRGKGAPKLRGGGQGDQHVTVNIVTPTKLNDAQKEALHAFAEASGDKMVHPKKKGFFDKVKDALDVDMSKIIGIDLGTTNSAVAVLEGTESKIIANPEGNRTTPSVVSFKNGEIIVGDAAKRQAVTNPDTVISIKSKMGTSEKVSANGKEYTPQEISAMILQYLKGYAEDYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLEVERIVNEPTAAALAYGMDKTDKDEKILVFDLGGGTFDVSILELGDGVFDVLATAGDNKLGGDDFDQKIIDFLVEEFKKENGIDLSQDKMALQRLKDAAEKAKKDLSGVTQTQISLPFITAGSAGPLHLEMSLSRAKFDDLTRDLVERTKTPVRQALSDAGLSLSEIDEVILVGGSTRIPAVVEAVKAETGKEPNKSVNPDEVVAMGAAIQGGVITGDVKDVVLLDVTPLSLGIETMGGVFTKLIDRNTTIPTSKSQVFSTAADNQPAVDIHVLQGERPMAADNKTLGRFQLTDIPAAPRGIPQIEVTFDIDKNGIVSVKAKDLGTQKEQHIVIQSNSGLTDEEIDKMMKDAEANAEADAKRKEEVDLKNEVDQAIFATEKTIKETEGKGFDTERDAAQSALDELKKAQESGNLDDMKAKLEALNEKAQALAVKLYEQAAAAQQAAQGAEGAQSADSSSKGDDVVDGEFTEKMSEEIKKDDLQEEVEATETEETVEEVIEEIPEKSELELANERADEFENKYLRAHAEMQNIQRRSSEERQQLQRYRSQDLAKAILPSLDNLERALAVEGLTDDVKKGLEMTRDSLIQALKEEGVEEVEVDSFDHNFHMAVQTLPADDEHPADSIAEVFQKGYKLHERLLRPAMVVVYNMITQRQNDILNLIVELFTQTHEPVGSKALQRTIDSSSATIRNDMAKLEKLGLLEKAHTSSGRMPSPAGFKYFVEHSLRLDSIDEQDIYHVIKAFDFEAFKLEDMLQKASHILSEMTGYTSVILDVEPARQRLTGFDVVQLSNHDALAVMTLDESKPVTVQFAIPRNFLTRDLIAFKAIVEERLLDGSVMDIHYKLRTEIPQIVQKYFVTTDNVLQLFDYVFSELFLETVFVAGKVNSLTYSDLSTYQFLDNEQQVAISLRQSLKEGEMASVQVADSQEAALADVSVLTHKFLIPYRGFGLLSLIGPIDMDYRRSVSLVNIIGKVLAAKLGDYYRYLNSNHYEVHMSYSNLKLFALSSNKELAKKVSQTIGIPLGQSTVRQFSDGEIQVNIEESIRGHHVFILQSTSSPVNDNLMEILIMVDALKRASAESVSVVMPYYGYARQDRKARSREPITSKLVANMLEVAGVDRLLTVDLHAAQIQGFFDIPVDHLMGAPLIADYFDRQGLVGDDVVVVSPDHGGVTRARKLAQCLKTPIAIIDKRRSVTKMNTSEVMNIIGNIKGKKCILIDDMIDTAGTICHAADALAEAGATAVYASCTHPVLSGPALDNIQNSAIEKLIVLDTIYLPEERLIDKIEQISIAELIGEAIIRIHEKRPLSPLFEMNKLKMTKNLLLTGFLSFNDGKLDTNYFSCIIKYIISYQEVMMTLEKRFNKYLDRIEVSLIRQFDQSISDIPGMVKLTLGEPDFTTPDHVKEAAKSAIDANQSYYTGMSGLLALRQAAADFAKDKYNLTYNPDCEILVTIGATEALSASLIAILEAGDVVLLPAPAYPGYEPIVNLVGADIVEIDTRENDFRLTPEMLETAIIQQGEKLKAVLLNYPTNPTGITYSRQEIAALAEVLKKYDIFVISDEVYSELTYTGQQHVSIAEYLPNQTILINGLSKSHAMTGWRVGLVYAPEAFIAQIIKSHQYMVTAASTISQFAGVEALSVGKNDTLPMRQGYIKRRDYIIDKMSKLGFKIIKPSGAFYIFAKIPDSYPQDSFKFCQDFAYQQAVAIIPGVAFGKYGEGYIRLSYAASMEVIETAMARLKVFMESYEGMRVSQTYGLVLYNRNYREDDKLVKIFTETEGKRMFFVKHASKSKFNAVLQPLTIAHFILKINDNGLSYIDDYKEVLAFQETNSDLFKLSYASYITSLADVAISDNVADAQLFIFLKKTLELIEDGLDYEILTNIFEVQLLERFGVALNFHDCVFCHRVGLPFDFSHKYSGLLCPNHYYKDERRNHLDPNMLYLINRFQSIQFDDLQTISVKPEMKLKIRQFLDMIYDEYVGIHLKSKKFIDDLSSWGSIMKSDMNKWLVKASSLVVLGGMVLSAGSRVLADTYVRPIDNGRITTGFNGYPGHCGVDYAVPTGTIIRAVADGTVKFAGAGANFSWMTDLAGNCVMIQHADGMHSGYAHMSRVVARTGEKVKQGDIIGYVGATGMATGPHLHFEFLPANPNFQNGFHGRINPTSLIANVATFSGKTQASAPSIKPLQSAPVQNQSSKLKVYRVDELQKVNGVWLVKNNTLTPTGFDWNDNGIPASEIDEVDANGNLTADQVLQKGGYFIFNPKTLKTVEKPIQGTAGLTWAKTRFANGSSVWLRVDNSQELLYKMIETMSLDDMREYLGQDQIPEDFDDFWKKQTMKYQGNIEYRLDKKDFNITFAQAYDLHFKGSNNSIVYAKCLFPKTNKPYPVVFYFHGYQNQSPDWSDQLNYVAAGYGVVSMDVRGQAGQSQDKGHFDGITVKGQIVRGMISGPNHLFYKDIYLDVFQLIDIIATLESVDSNQLYSYGWSQGGALALIAAALNPKIVKTVAVYPFLSDFRRVLDLGGVSEPYDELFRYFKYSDPFHKTENNVLKTLAYIDVKNFAHRISCPVVLLTALKDDICPPSTQFAIFNRLTSTKKHLLLPDYGHDPMTVQVKDHIFDQLTGSQFTKQKIEMTRTVAIDIGGTMIKHGIVDNLGCIVEASELATEAYKGGPGILQKVCQIIDNYLAEGSIDGIAISSAGMVDPDEGCIFYSGPQIPNYAGTQFKKVLEDTYQVRTEIENDVNCAGLAEAVSGSAKDSSIALCLTIGTGIGGCLIIDKTVFHGFSNSACEVGYMHLSDGDFQDLASTTALIADVAKAHGDEISRWDGRRIFQEAKKGNEKCIASIDRMINYLGQGIANMVYVVNPEKVVLGGGIMAQKDYLQDKLSESLKRNLVTSLAEKTAIVFAQHENQAGMLGAYYHFKNRGMKDLQKYQGIIPAFYACYDDKGDICPERVKALTNYFIDKGVQGLYVNGSSGECIYQSVADRKLVLENVMSVAKGKLTVIAHVACNNTKDSVELAMHAEAIGVDAIAAIPPIYFRLPEYAIADYWNTISQAAPQTDFIIYNIPQLAGVALTSDLYRKMLQNPQVIGVKNSSMPVQDIQNFVAIGGENHIVFNGPDEQFLGGRLMGAAAGIGGTYGVMPELYLTLNQLIVDKDLEKARELQFTINDIITKLCSGHGNMYAVIKAVLEINEQLTIGSVRLPLASVTEEDKPIIKEAAEMIRHAKKQFCMKKANQLIAAIFDVNNPFMQGCNVVFDLALLNLLFMITCLPLVTIGAAKISLYRTLWQKLEGDQTNLLILYIKHLKKEWFQGMLLGLVELSILVVIIFDLTILHYQIGFIVSFLKITCYAFLLLTVMTSIYLFPMAARYEMSLLDTVKKSFIMACLNLKWTGVLMFLLIMTWFIMVQSSLLFMLTVSAIFIFAYTAFAYFKIIILQKQFAYFSKQQGDYQMIYDHLLNLTHYKDINPNLDLAIDYLLSHDLRNLDIGTYHISPEVILMVQSNQLSESFDHIFEYHKKYLDIHYVIEGHEVIKLGKGDKVEVEEYLGDIGFIKCSEETSFDLRDNYIAFFFPEEAHQPNGMGSLGNYVKKGVLKVLMAMKKKTFSAYNFLTALILCLLTVLFIFPFYWIMTGAFKSQPDTIIIPPQWWPKAPTLENFKALTVQNPALRWLWNSVFISIMTMFLVCCTSSMAGYVLAKKRFYGQKILFSLFIAAMALPKQVVLVPLVRIINFMGIHDTLWAVILPLVGWPFGVFLMKQFSENIPTELLESAKIDGCGEIRTFINVAFPIVKPGFAALAIFTFINTWNDYFMQLVMLTSRNNLTISLGVATMQAEMATNYGLIMAGAALAAVPIVTVFLVFQKSFTQGITMGAVKGMRTNKLKMRETMIAYAFLAPILLFFLIFVFAPMVMGFVTSFFNYSMTQFTFIGLANYNRMFHDSIFMKSLINTVIIVIGSVPVVVFFSLFVAANTYEKNVFSRSFYRCVFFLPVVTGSVAVTVVWKWIYDPMSGILNYILKSGHVIEQNISWLGDKHWALLAIIIILLTTSVGQPIILYIAAMGNIDNSLCEAARVDGANEMQVFWQIKWPSLLPTTLYIAVITTINSFQCFALIQLLTSGGPNYSTSTLMYYLYEKAFKLSEYGYANTMGVFLAVMIALISFAQFKILGNDVEYMSIKKSVIGFCLGAAALSMFACVDSSQSVMAAEKDKVEITWWAFPTFTQEKAKDGVGTYEKKVIKAFEKKNPNIKVKLETIDFTSGPEKITTAIEAGTAPDVLFDAPGRIIQYGKNGKLADLNDLFTDQFIKDVNNKNIIQASKSGDKAYMYPISSAPFYMAFNKKMLKDAGVLKLVKEGWTTSDFEKVLKALKNKGYTPGSFFANGQGGDQGPRAFFANLYSAPITDKEVTKYTTDTKNSVKSMKKIVEWIKKGYLMNGSQYDGSADIQNFANGQTAFTILWAPAQPKTQAKLLESSKVDYLEVPFPSEDGKPDLEYLVNGFAVFNNKDENKVKASKKFITFIADDKKWGPKDVIRTGAFPVRTSFGDLYKGDKRMMKISKWTQYYSPYYNTIDGFSEMRTLWFPMVQSVSNGDEKPADALKDFTQKANDTIKKAAKMPHLSKEAFKKQIKNGIIVSCQALPGEPLYTESGGVMPLLALAAQEAGAVGIRANSVRDIKEIQEVTNLPIIGIIKREYPPQEPFITATMTEVDQLASLDIAVIALDCTLRERHDGLSVVEFIQKIKRKYPEQLLMADISTFEEGKNAFEAGVDFVGTTLSGYTDYSRQEEGPDIELLNKLCQAGIDVIAEGKIHTPKQANEINHIGVAGIVVGGAITRPKEIAERFISGLSMKMNKKVLLTSTMAASLLSVASVQAQETDTTWTARTVSEVKADLVKQDNKSSYTVKYGDTLSVISEAMSIDMNVLAKINNIADINLIYPETTLTVTYDQKSHTATSMKIETPATNAAGQTTATVDLKTNQVSVADQKVSLNTISEGMTPEAATTIVSPMKTYSSAPALKSKEVLAQEQAVSQAAANEQVSPAPVKSITSEVPAAKEEVKPTQTSVSQSTTVSPASVAAETPAPVAKVAPVRTVAAPRVASVKVVTPKVETGASPEHVSAPAVPVTTTSPATDSKLQATEVKSVPVAQKAPTATPVAQPASTTNAVAAHPENAGLQPHVAAYKEKVASTYGVNEFSTYRAGDPGDHGKGLAVDFIVGTNQALGNKVAQYSTQNMAANNISYVIWQQKFYSNTNSIYGPANTWNAMPDRGGVTANHYDHVHVSFNKMTKRALISVSDKSGIIDFAKELKNLGWDIISTGGTKVALDDAGVETIAIDDVTGFPEMMDGRVKTLHPNIHGGLLARRDADSHLQAAKDNNIELIDLVVVNLYPFKETILRPDVTYDLAVENIDIGGPSMLRSAAKNHASVTVVVDSADYATVLGELADASQTTFKTRQRLAAKAFRHTAAYDALIAEYFTAQVGEAKPEKLTITYDLKQAMRYGENPQQDADFYQKALPTDYSIASAKQLNGKELSFNNIRDADAAIRIIRDFKDSPTVVALKHMNPCGIGQADDIETAWDYAYEADPVSIFGGIVVLNREVDAATAEKMHPIFLEIIIAPSYSEEALAILTNKKKNLRILELPFDAQAASEVEAEYTGVVGGLLVQNQDVVAENPSDWQVVTDRQPTEQEATALEFAWKAIKYVKSNGIIITNDHMTLGLGAGQTNRVGSVKIAIEQAKDHLDGAVLASDAFFPFADNIEEIAAAGIKAIIQPGGSVRDQESIDAANKHGLTMIFTGVRHFRHMELIFRIFEMKKTLYITNKLFFANWFVPVIGAVLIQVIGIIVSRRLVVKLLPDDYKFNLYIALLLFVPILASILLFLIYFQKRDFTSLGFTKDNNVLTTISGFITGSLLMFFIYICHWLSGFVEISSSNSFSFGPFFFLFLAYFIQSLTEEILFRGYVMTTVTKFKGSFAGVLCNSMLFSFIHFRNYGITAIALFNLFLLGIIFSILFNMTKNILFVTGVHTTWNFTMGCVLGNKVSGGDSPVSLFRITENSSFALWNGGDFGFEGGVLCSLILVGCLAYFSLESVRVSVRYMKLVKNLEIVESIFGDWDETIIWSCVQGIMGEVFVDSLDQPKSSLAKLGRKSSFGFLAGQPTLFLLEVCSGEDIILVPQHKGWSDLIESTYGQNAHSFKRYATKKDTLFERSRLEKFVTQLPNGFELRAIDEKVYNSCLEKEWSQDLVANYATYQYYKKQGIGYVVYYQGNIIAGASSYSTYKNGIEIEVDTHPDFRRRGLATIVAAQLILTCLDKGIYPSWDAHTRTSLNLSEKLGYEFSHEYIAYEIDMKIAVFASGNGSNFQVIAEQFQVSFVFSDHRDAYVLERAQNLAIPSFAFELKEFENKAAYEQAVVDLLDKHEIDLVCLAGYMKIVGETLLSAYEGRIINIHPTYLPEFPGAHGIKDAWEAGVDQSGVTIHWVDSGVDTGQVIQQVHVPRLADDSLESFETRIHETEYQLYPAVLDSLGIKRKMMSNMTLYIIANPHAGNKNASTIVGKIQELYHTEDISVFYTEQKDDEKKQVINILRSFKESDHLMIIGGDGTLSKVMTYLPQHIPCTYYPVGSGNDFARALKIPNLKETLTAIQTERLKEINCFIYDKGLILNSLDLGFAAYVVWKASNSKIKNILNRYRLGKITYIVIAIKSLLHSSKVQVLVEGETGQQIKLNDLYFFALANNTYFGGGITIWPKASALTAELDMVYAKGHTFLKRLSILLSLVFKRHTTSKSIKHQTFKAMTVYFPKNSLIEIDGEIVELDQISLKCQKRYLYMMSEKNAYAQSGVDVEAGYEVVERIKKHVARTERAGVMGALGGFGGMFDLSQTGVKEPVLISGTDGVGTKLMLAIKYDKHDTIGQDCVAMCVNDIIAAGAEPLYFLDYVATGKNEPAKLEQVVAGVAEGCVQASAALIGGETAEMPGMYGEDDYDLAGFAVGVAEKSQIIDGSKVKEGDILLGLASSGIHSNGYSLVRRVFADYTGDEVLPELEGKQLKDVLLEPTRIYVKAALPLIKEELVNGIAHITGGGFIENVPRMFADDLAAEIDEDKVPVLPIFKALEKYGDIKHEEMFEIFNMGVGLMLDVNPENVDRVKELLDEPVYEIGRIIKKADDSVVIKMTYEVKSLNEECGVFGIWGYPQAAQVTYFGLHSLQHRGQEGAGIISNDNGKLYGYRNVGLLSEVFKNQSELDNLTGNAAIGHVRYATAGSADIRNIQPFLYKFHDGQFALCHNGNLTNAISSRKELEKQGAIFNASSDTEILMHLIRRSHNPSFMGKVKEALSTVKGGFAYLLMTEDKLIAALDPNAFRPLSIGQMQNGAWVISSETCAFEVVGAKWVRDVEPGEVILIDDSGIQCDRYTDETQLAICSMEYVYFARPDSTIHGVNVHTARKNMGKRLAQEFKQDADIVIGVPNSSLSAAMGFAEESGLPNEMGLVKNQYTQRTFIQPTQELREQGVRMKLSAVSGVVKGKRVVMIDDSIVRGTTSRRIVGLLREAGATEVHVAIASPELKYPCFYGIDIQTRRELISANHAVDEVCDIIGADSLTYLSIDGLIKSIGLETKAPNGGLCVAYFDGHYPTPLYDYEEEYLRSLEEKTSFYIQKVKMNKRIFVEKKADFGIKSASLVKELTHNLQLASLKDLRIVQVYDVFNLAEDLLARAEKHIFSEQVTDRLLTEAEITAELDKVAFFAIEALPGQFDQRAASSQEALLLLGSDSQVKVNTAQLYLVNKDIAEAELEAVKNYLLNPVDSRFKDITLPLEVQAFSVSDKTISNLDFFETYQADDFAAYKAEQGLAMEVDDLLFIQDYFKSIGRVPTETELKVLDTYWSDHCRHTTFETELKNIDFSASKFQKQLQATYDKYIAMRDELGRSEKPQTLMDMATIFGRYERANGRLDDMEVSDEINACSVEIEVDVDGVKEPWLLMFKNETHNHPTEIEPFGGAATCIGGAIRDPLSGRSYVYQAMRISGAGDITTPIAETRAGKLPQQVISKTAAHGYSSYGNQIGLATTYVREYFHPGFVAKRMELGAVVGAAPKENVVREKPEAGDVVVLLGGKTGRDGVGGATGSSKVQTVESVETAGAEVQKGNAIEERKIQRLFRDGNVTRLIKKSNDFGAGGVCVAIGELADGLEIDLDKVPLKYQGLNGTEIAISESQERMSVVVGPSDVDAFIAACNKENIDAVVVATVTEKPNLVMTWNGETIVDLERCFLDTNGVRVVVDAKVVDKDLTVPEARTTSAETLEADMLKVLSDLNHASQKGLQTIFDSSVGRSTVNHPIGGRYQITPTESSVQKLPVQYGVTTTASVMAQGYNPYIAEWSPYHGAAYAVIEATARLVATGADWSRARFSYQEYFERMDKQAERFGQPVSALLGSIEAQIQFGLPSIGGKDSMSGTFEELTVPPTLVAFGVTTADSRKVLSPEFKAAGENIYYIPGQAISEDIDFDLIKANFSQFEAIQAQHKITAASAVKYGGVLESLALMTFGNRIGASVEIAELDSSLTAQLGGFVFTSVEEIADVVKIGQTQADFTVTVNGNDLAGASLLSAFEGKLEEVYPTEFEQVDAIEEVPAVVSDVVIKAKEIIEKPVVYIPVFPGTNSEYDSAKAFEQVGASVNLVPFVTLNEAAIAESVDTMVANIAKANIIFFAGGFSAADEPDGSAKFIVNILLNEKVRAAIDSFIEKGGLIIGICNGFQALVKSGLLPYGNFEEAGETSPTLFYNDANQHVAKMVETRIANTNSPWLAGVEVGDIHVIPVSHGEGKFVVSASEFAELRDNGQIWSQYVDFDGQPSMDSKYNPNGSVNAIEGITSKNGQIIGKMGHSERWEDGLFQNIPGNKDQKLFESAVKYFTGKMTNQLIYTGKAKDIYSTKDENVIRTVYKDQATMLNGARKETIDGKGALNNQISSLIFEKLNMAGVVTHYIEQISKNEQLNKKVDIIPLEVVLRNVTAGSFSKRFGVEEGHVLETPIVEFYYKNDNLNDPFINDEHVKFLGIVNDEEIAYLKGETRHINELLKDWFAQIGLNLIDFKLEFGFDKDGKIILADEFSPDNCRLWDADGNHMDKDVFRRDLGSLTDVYQVVLEKLIALMSRDEVFEKMLELLRQQLGDPQLDITPESSLHDDLAIDSIALTEFIINLEDVFHLEIPDEAVEHMSSVQQLLDYIIEHKMKKIAIDAMGGDYAPKAIVEGVNQAISDFSDIEVQLYGDQKKIEKYLTVTERVSIIHTEEKINSDDEPAKAVRRKKQSSMVLGAKAVKDGVAQAFISAGNTGALLAAGLFVVGRIKGVDRPGLMSTMPTLDGVGFDMLDLGANAENTASHLHQYAILGSFYAKNVRGIEVPRVGLLNNGTEETKGDSLHKEAYELLAAEPSINFIGNIEARDLMSSVADVVVTDGFTGNAVLKTMEGTAMSIMGSLKSSIKSGGVKAKLGALLLKDSLYQLKDSMDYSSAGGAVLFGLKAPIVKCHGSSDSKAVYSTLKQVRTMLETQVVDQLVDAFTDEMRKRFSLLNFIVVTFIFFFFILFPLLNHKGKVDANSRQSVTYTKEEFIQKIVPDAQDLGKSYGIRPSFIIAQAALDSDFGEKILANKYHNLFGLLAEPGTPSITLNDSSTGKKQEKQFTHYKSWKYSMYDYLAHIKSGATGKKDSYTIMVSVKNPKTLVQKLQDSGFDNDKKYAKKMTEIIDLYDLTRYDK

From eabe30663e8938f92a75fbce7bd6e6e7e17092d4 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 5 Apr 2024 15:07:30 +0200
Subject: [PATCH 69/97] help is edited

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 92bcc0866af..6b6cf96d9c5 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -81,12 +81,6 @@ chewBBACA is a software suite for the creation and evaluation of core genome and
 
 The AlleleCallEvaluator module allows users to generate an interactive HTML report to evaluate allele calling results generated by the AlleleCall module. The report provides summary statistics to evaluate results per sample and per locus (with the possibility to provide a TSV file with loci annotations to include on a table). The report includes components to display a heatmap representing the loci presence-absence matrix, a heatmap representing the distance matrix based on allelic differences and a Neighbor-Joining (NJ) tree based on the MSA of the core genome loci.
 
-.. class:: infomark
-
-**Note**
-
-You have to uncompress the archive and open the HTML file with a browser.
-
 .. class:: warningmark
 
 **Warning**

From edce4448a25ef88cec24a40b95e9b0fd7d183753 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 8 Apr 2024 15:41:39 +0200
Subject: [PATCH 70/97] the output is now an html file not a collection

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 24 +++++++-----------------
 1 file changed, 7 insertions(+), 17 deletions(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 6b6cf96d9c5..9a266714a11 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -6,7 +6,7 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir 'input' &&
-        mkdir 'schema' &&
+        mkdir -p 'schema' &&
         #for $file in $input_file
         ln -sf '$file' 'input/${file.element_identifier}.tsv' &&
         #end for
@@ -30,7 +30,9 @@
             #if 'cg-alignment' in $computation:
                 --cg-alignment
             #end if
-            -i 'input' -g 'schema/schema_seed/' -o 'output'
+            -i 'input' -g 'schema/schema_seed/' -o '${html_file.files_path}'
+            && cp '${html_file.files_path}'/*\.html output.html
+
     ]]></command>
     <inputs>
         <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
@@ -47,9 +49,7 @@
         </section>
     </inputs>
     <outputs>
-        <collection name="output_collection" type="list" format="tsv,fasta,js,html" label="${tool.name} on ${on_string}">
-            <discover_datasets pattern="__name_and_ext__" directory="output"/>
-        </collection>
+        <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage" />
     </outputs>
     <tests>
         <test expect_exit_code="0">
@@ -62,18 +62,8 @@
                 </collection>
             </param>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
-            <output_collection name="output_collection" type="list">
-                <element name="allelecall_report" file="allelecall_report.html">
-                    <assert_contents>
-                        <has_text_matching expression="report_bundle.js"/>
-                    </assert_contents>
-                </element>
-                <element name="cgMLST_MSA" file="cgMLST_MSA.fasta">
-                    <assert_contents>
-                        <has_text_matching expression="GCA_000007265"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
+            <output name="html_file" file="allelecallevaluator_report.html" ftype="html" compare="sim_size">
+            </output>
         </test>
     </tests>
     <help>

From fcca0f8289da7ed20e4ef103a7928265a96f7bad Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 8 Apr 2024 15:49:04 +0200
Subject: [PATCH 71/97] corrected output filtering in AlleleCall.xml

---
 tools/chewbbaca/AlleleCall.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index aec9beedeb8..4acb53950bb 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -96,17 +96,17 @@
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" format="txt" directory="output"/>
         </collection>
         <data name="unclassified_fasta" format="fasta" from_work_dir="output/unclassified_sequences.fasta" label="${tool.name} on ${on_string}: Unclassified fasta">
-            <filter>output_selector['output_unclassified']</filter>
+            <filter>output['output_selector'] and 'output_unclassified' in output['output_selector']</filter>
         </data>
         <data name="missing_fasta" format="fasta" from_work_dir="output/missing_classes.fasta" label="${tool.name} on ${on_string}: Missing fasta">
-            <filter>output_selector['output_missing']</filter>
+            <filter>output['output_selector'] and 'output_missing' in output['output_selector']</filter>
         </data>
         <data name="novel_fasta" format="fasta" from_work_dir="output/novel_alleles.fasta" label="${tool.name} on ${on_string}: Novel fasta">
-            <filter>output_selector['output_novel']</filter>
+            <filter>output['output_selector'] and 'output_novel' in output['output_selector']</filter>
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="4">
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
             <param name="output_selector" value="output_unclassified,output_missing,hash_profile" />

From 5dca75356e408f86018bd3cd578f742611eff4c0 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Mon, 8 Apr 2024 15:49:34 +0200
Subject: [PATCH 72/97] update test-data

---
 .../test-data/allelecallevaluator_report.html    | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 tools/chewbbaca/test-data/allelecallevaluator_report.html

diff --git a/tools/chewbbaca/test-data/allelecallevaluator_report.html b/tools/chewbbaca/test-data/allelecallevaluator_report.html
new file mode 100644
index 00000000000..423fe059c6e
--- /dev/null
+++ b/tools/chewbbaca/test-data/allelecallevaluator_report.html
@@ -0,0 +1,16 @@
+
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>AlleleCall Report - React Edition</title>
+</head>
+<body style="background-color: #f6f6f6">
+    <noscript> You need to enable JavaScript to run this app. </noscript>
+    <div id="root"></div>
+    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"], "loci_data": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 104, 114]]}], "loci_stats": [{"columns": ["Locus", "Total CDSs", "Valid Classes", "Invalid Classes", "Proportion Samples", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [["GCA-000007265-protein1", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein58", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein67", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein66", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein65", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein64", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein63", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein62", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein61", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein60", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein6", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein59", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein57", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein69", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein56", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein55", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein54", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein53", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein52", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein51", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein50", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein5", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein49", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein48", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein68", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein7", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein10", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein84", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein98", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein97", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein96", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein95", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein94", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein93", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein9", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein87", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein86", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein85", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein82", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein70", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein81", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein80", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein8", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein79", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein77", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein76", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein75", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein74", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein72", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein71", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein47", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein46", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein45", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein44", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein2", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein19", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein14", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein13", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein12", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein114", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein113", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein112", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein111", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein110", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein11", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein109", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein108", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein107", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein106", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein105", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein104", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein103", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein102", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein101", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein100", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein20", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein21", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein22", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein33", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein43", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein42", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein41", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein40", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein39", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein38", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein37", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein36", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein35", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein34", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein32", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein23", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein31", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein30", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein3", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein29", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein28", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein27", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein26", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein25", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein24", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein99", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein16", 3, 0, 1, 0.0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "annotations": [{"columns": []}, {"rows": []}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265:0.000000000);\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>
+    <script src="./report_bundle.js"></script>
+</body>
+</html>
+

From bcf0d83e2d2c94ad5603f2034eec24a5f3983291 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 9 Apr 2024 11:34:26 +0200
Subject: [PATCH 73/97] --cds-input is boolean now

---
 tools/chewbbaca/CreateSchema.xml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 0053d0786fe..d32dd390865 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -13,9 +13,7 @@
             #if $training_file:
                 --ptf '$training_file'
             #end if
-            #if $cds_input:
-                --cds '$cds_input'
-            #end if
+            $cds_input
             @COMMON_INPUT@
             --pm $prodigal_mode
             -i 'input' -o 'output' &&
@@ -26,7 +24,7 @@
         <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
-            <param argument="--cds-input" type="data" format="txt" label="CDS input" optional="true" />
+            <param argument="--cds-input" type="boolean" truevalue="--cds-input" falsevalue="" checked="false" label="CDS input" optional="true"/>
             <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
             <expand macro="common_param" />
             <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help="&quot;single&quot; for finished genomes, reasonable quality draft genomes and big viruses. &quot;meta&quot; for metagenomes, low quality draft genomes, small viruses, and small plasmids">

From e011a5701b9e5ab826c31d1733c1940f16776aca Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 9 Apr 2024 12:09:15 +0200
Subject: [PATCH 74/97] added a test for --cds in CreateSchema.xml

---
 tools/chewbbaca/CreateSchema.xml              |  5 ++++
 .../test-data/CDS_Str_agalactiae.fasta        | 28 +++++++++++++++++++
 2 files changed, 33 insertions(+)
 create mode 100644 tools/chewbbaca/test-data/CDS_Str_agalactiae.fasta

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index d32dd390865..24b6c53a8a8 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -60,6 +60,11 @@
             <param name="training_file" value="Streptococcus_agalactiae.trn"/>
             <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed_trn.zip" compare="sim_size"/>
         </test>
+        <test expect_num_outputs="1">
+            <param name="input_file" value="CDS_Str_agalactiae.fasta"/>
+            <param name="cds_input" value="true"/>
+            <output name="schema" file="Str_agalactiae_cds.zip" compare="sim_size"/>
+        </test>
     </tests>
     <help>
         
diff --git a/tools/chewbbaca/test-data/CDS_Str_agalactiae.fasta b/tools/chewbbaca/test-data/CDS_Str_agalactiae.fasta
new file mode 100644
index 00000000000..3896288998f
--- /dev/null
+++ b/tools/chewbbaca/test-data/CDS_Str_agalactiae.fasta
@@ -0,0 +1,28 @@
+>FJ801036.1 Streptococcus agalactiae strain ABC020023529 BibA gene, complete cds
+ATGAATAATAACGAAAAAAAAGTAAAATACTTTTTAAGAAAAACAGCTTATGGTTTGGCTTCAATGTCAG
+CGGCGTTTATAGTATGTAGTGGTATTGTAAATACTCCTACAGTGTCTGCTGATAGTCCTGATACATTAAA
+AGTCGAAAAATTAGGCAAATTGAAAGATGTGAAATCAGTTCATGAACTCACACCCATATCAATACCGAAC
+GAATTAAAAGGTGCTAAAGAGCAAGCACTTTCTTCAATAATTTCACATCCTAATATAACTAATTCGGAAG
+TAGACAAACTAGCTAGTGACTATAGTTTTAGAATTAATACATCTAATGATGTGAACGACGTTAAACGTCT
+ATTAAATGAATTTTATAACGCAGTTGCAAGGAAACAGTTAGATACAAATTCTGCTGACTACCGTAGTAAA
+ATTGATAATATCAGTACTACAGGTCTTGCGATAGCTCTTGAGGCTAAAGAAATTTATGAAGCAAATAAAT
+CTATATTACCTCATCGTTACAAAGATTCTGTTGGAACTTATGTGAACAGTTTTGAGGAAAGACGAAGTCC
+AGGAAAATTTAATATTTGGAATGGTCAGGAAGGATTTAATGCAGCTCAAAAATTGTTAGAAGATGTTAAA
+AAATTATTACTTGAGCTACAAAATTTAACAAAAAATAACAAACCAAATATTCAAGTACCTAAACAAGCAC
+CTACAGAAGCTGCAAAACCAGCTTTGTCACCAGAAGCCTTGACAAGATTGACTACATGGTATAATCAAGC
+TAAAGATCTGCTTAAAGATGATCAAGTAAAGGACAAATACGTAGATATACTTTCAGTTCAAAAAGCTGTT
+GACCAAGCTTATGATCATGTGGAAGAGGGAAAATTTATTACCACTGATCAAGCAAATCAATTAGCTAACA
+AGCTACGTGATGCTTTACAAAGTTTAGAATTAAAAGATAAAAAAGTAGCCAAACCAGTAGCTAAAGGTAC
+ATACGATGTTAAGTATGTAGACACAGAAGGAAAAGAAGTAGCTAAGTCACGTCACTTCGAAGGAGAAGAA
+GGCGCAGCTTTTGTCACTTCAGCGAAAGAAGTAGCGGGTTACAAACTTGTTAGAACGGAAGGCGCTGTTT
+CAAATGTCTTCACAGCAGGAGCACAAGTACGTACATATGTTTACGAAAAAGTAGCCAAACCAGTAGCTAA
+AGGTACATACGATGTTAAGTATGTAGACACAGAAGGAAAAGAAGTAGCTAAGTCGCGTCACTTCGAAGGA
+GAAGAAGGCGCAGCTTTTGTCACTTCAGCGAAAGAAGTAGCGGGTTACAAACTTGTTAGAACGGAAGGTG
+CTGTTTCAAATGTCTTCACAGCAGGAGCACAAGTACGTACATATGTTTACGAAAAAGTTAAACCAGAAGT
+TAAACCAGACGTTAAGCCAGAGGCCAAACCAGAGGCTAAGCCAGAAGTTAAACCAGACGTTAAGCCAGAG
+GCCAAACCAGAGGCTAAGCCAGAAGTTAAATCAGACGTTAAGCCAGAGGCTAAGCCAGAAGCCAAACCAG
+AGGCTAAACCAGAAGTTAAACCAGACGTTAAGCCAGAGGCTAAACCAGAAGCCAAGCCAGCAACCAAAAA
+ATCGGTTAATACTAGCGGAAACTTGGTGGCTAAAAAAGCTATTGAAAACAAAAAGTATAGTAAAAAATTA
+CCATCAACGGGTGAAGCCGCAAGTCCACTCTTAGCAATTGTATCACTAATTGTTATGTTAAGTGCAGGTC
+TTATTACGATAGTTTTAAAGCATAAAAAAAATTAA
+

From 93c772230ba6c2ad8d00fe02a899ae2af16bbad7 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 9 Apr 2024 12:14:14 +0200
Subject: [PATCH 75/97] update test data

---
 tools/chewbbaca/test-data/Str_agalactiae_cds.zip | Bin 0 -> 2519 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 tools/chewbbaca/test-data/Str_agalactiae_cds.zip

diff --git a/tools/chewbbaca/test-data/Str_agalactiae_cds.zip b/tools/chewbbaca/test-data/Str_agalactiae_cds.zip
new file mode 100644
index 0000000000000000000000000000000000000000..0de5745e04afe109634b90d7bbb4770419165b7d
GIT binary patch
literal 2519
zcmWIWW@h1H0D&t3oe^LLl;B~IVJJ?{NX<=*FHTKO(GLybWMI}87EJ@;(h6<{MwYF<
z3=Ay2EDQ_*KvP73`Z&O*%=>D|qr$|%Aj!_apo?aTvrDjUa7mGFVtQguVsc4lVybRI
zQGQ8kW}cy5T4HfYB0g)jhI(g72k_i^t{3-&iFM&28HHQy!akfWOIYsD&q`Cd&e^DU
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From b7a76b947d823570473b821f5828af09aded2c59 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Tue, 9 Apr 2024 14:10:58 +0200
Subject: [PATCH 76/97] --cds is boolean for AlleleCall.xml

---
 tools/chewbbaca/AlleleCall.xml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 4acb53950bb..630b44bb77b 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -15,9 +15,7 @@
             #if $training_file:
                 --ptf '$training_file'
             #end if
-            #if str($cds_input) != 'None'
-                --cds '$cds_input'
-            #end if
+            $cds_input
             #if $genes_list:
                 --gl '$genes_list'
             #end if
@@ -58,7 +56,7 @@
         <section name="advanced" title="Advanced options">
             <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" help="By default, gets the training file from the schema"/>
-            <param argument="--cds-input" type="data" format="txt" label="CDS input" optional="true" />
+            <param argument="--cds-input" type="boolean" truevalue="--cds-input" falsevalue="" checked="false" label="CDS input" optional="true"/>
             <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="" optional="true" label="BLAST Score Ratio value" /> 
             <param argument="--minimum-length" type="integer" min="0" value="" optional="true" label="Minimum sequence length value"/>
             <param argument="--translation-table" type="integer" min="0" value="" optional="true" label="Genetic code used to predict genes and to translate coding sequences"/>

From 6203ca7d5fba5697ed2c31e01eef990c789be4e5 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 10 Apr 2024 15:34:04 +0200
Subject: [PATCH 77/97] added test for annotation file in
 AlleleCallEvaluator.xml

---
 tools/chewbbaca/AlleleCallEvaluator.xml            | 14 ++++++++++++++
 .../test-data/allelecallevaluator_report.html      |  2 +-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 9a266714a11..d1771b013fd 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -65,6 +65,20 @@
             <output name="html_file" file="allelecallevaluator_report.html" ftype="html" compare="sim_size">
             </output>
         </test>
+        <test expect_exit_code="0">
+            <param name="input_file">
+                <collection type="list">
+                    <element name="cds_coordinates" value="cds_coordinates.tsv" ftype="tabular"/>
+                    <element name="loci_summary_stats" value="loci_summary_stats.tsv" ftype="tabular"/>
+                    <element name="results_alleles" value="results_alleles.tsv" ftype="tabular"/>
+                    <element name="results_statistics" value="results_statistics.tsv" ftype="tabular"/>
+                </collection>
+            </param>
+            <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <param name="annotations" value="schema_seed_annotations.tsv"/>
+            <output name="html_file" file="allelecallevaluator_report.html" ftype="html" compare="sim_size">
+            </output>
+        </test>
     </tests>
     <help>
 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
diff --git a/tools/chewbbaca/test-data/allelecallevaluator_report.html b/tools/chewbbaca/test-data/allelecallevaluator_report.html
index 423fe059c6e..fb8d807fbf4 100644
--- a/tools/chewbbaca/test-data/allelecallevaluator_report.html
+++ b/tools/chewbbaca/test-data/allelecallevaluator_report.html
@@ -9,7 +9,7 @@
 <body style="background-color: #f6f6f6">
     <noscript> You need to enable JavaScript to run this app. </noscript>
     <div id="root"></div>
-    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", 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+    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", 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["GCA-000007265-protein47", "GCA_000007265", "AE009948.1", "60012", "61103", "47", "1", "N5-carboxyaminoimidazole ribonucleotide synthase", "http://purl.uniprot.org/uniprot/A0A0E1EJA7", "", "", "", "", ""], ["GCA-000007265-protein99", "GCA_000007265", "AE009948.1", "102830", "103405", "99", "1", "Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain-containing protein", "http://purl.uniprot.org/uniprot/Q8E7R0", "", "", "", "", ""], ["GCA-000007265-protein102", "GCA_000007265", "AE009948.1", "105338", "107167", "102", "1", "Chaperone protein DnaK", "http://purl.uniprot.org/uniprot/P0A3J2", "", "", "", "", ""], ["GCA-000007265-protein96", "GCA_000007265", "AE009948.1", "100791", "101270", "96", "1", "Competence-specific sigma factor ComX", "http://purl.uniprot.org/uniprot/Q8E7R3", "", "", "", "", ""], ["GCA-000007265-protein66", "GCA_000007265", "AE009948.1", "79871", "80524", "66", "1", "Small ribosomal subunit protein uS3", "http://purl.uniprot.org/uniprot/A2RC20", "", "", "", "", ""], ["GCA-000007265-protein20", "GCA_000007265", "AE009948.1", "30369", "31337", "20", "1", "Ribose-phosphate pyrophosphokinase 1", "http://purl.uniprot.org/uniprot/Q8E2H0", "", "", "", "", ""], ["GCA-000007265-protein57", "GCA_000007265", "AE009948.1", "73207", "74697", "57", "1", "Threonine synthase", "http://purl.uniprot.org/uniprot/A0A0E1EJC0", "", "", "", "", ""], ["GCA-000007265-protein42", "GCA_000007265", "AE009948.1", "55017", "55898", "42", "1", "N-acetylmannosamine kinase", "http://purl.uniprot.org/uniprot/A0A0E1EJA4", "", "", "", "", ""], ["GCA-000007265-protein14", "GCA_000007265", "AE009948.1", "13935", "15911", "14", "1", "ATP-dependent zinc metalloprotease FtsH", "http://purl.uniprot.org/uniprot/Q8E7Y0", "", "", "", "", ""], ["GCA-000007265-protein76", "GCA_000007265", "AE009948.1", "84290", "84646", "76", "1", "Large ribosomal subunit protein uL18", "http://purl.uniprot.org/uniprot/Q3K3V3", "", "", "", "", ""], ["GCA-000007265-protein98", "GCA_000007265", "AE009948.1", "102081", "102833", "98", "1", "Peptidase M15B domain-containing protein", "http://purl.uniprot.org/uniprot/Q8E7R1", "", "", "", "", ""], ["GCA-000007265-protein64", "GCA_000007265", "AE009948.1", "79220", "79498", "64", "1", "Small ribosomal subunit protein uS19", "http://purl.uniprot.org/uniprot/Q1JE54", "", "", "", "", ""], ["GCA-000007265-protein52", "GCA_000007265", "AE009948.1", "66381", "66818", "52", "1", "protein-tyrosine-phosphatase", "http://purl.uniprot.org/uniprot/A0A0E1EJB3", "", "", "", "", ""], ["GCA-000007265-protein10", "GCA_000007265", "AE009948.1", "10295", "10666", "10", "1", "Cell division protein DivIC", "http://purl.uniprot.org/uniprot/Q8E7Y5", "", "", "", "", ""]]}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265:0.000000000);\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>
     <script src="./report_bundle.js"></script>
 </body>
 </html>

From 788e640bb38eb1c8a166ca9e11fdae8641e07fec Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 10 Apr 2024 15:58:55 +0200
Subject: [PATCH 78/97] updateed help for AlleleCall.xml ExtractCgMLST.xml

---
 tools/chewbbaca/AlleleCall.xml    | 2 +-
 tools/chewbbaca/ExtractCgMLST.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 630b44bb77b..483a8c0cb84 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -59,7 +59,7 @@
             <param argument="--cds-input" type="boolean" truevalue="--cds-input" falsevalue="" checked="false" label="CDS input" optional="true"/>
             <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="" optional="true" label="BLAST Score Ratio value" /> 
             <param argument="--minimum-length" type="integer" min="0" value="" optional="true" label="Minimum sequence length value"/>
-            <param argument="--translation-table" type="integer" min="0" value="" optional="true" label="Genetic code used to predict genes and to translate coding sequences"/>
+            <param argument="--translation-table" type="integer" min="0" value="" optional="true" help="Must match the genetic code used to create the training file (default: uses value defined in schema config)." label="Genetic code used to predict genes and to translate coding sequences"/>
             <param argument="--size-threshold" type="float" min="0" value="" optional="true" label="CDS size variation threshold"/>
             <param argument="--no-inferred" type="boolean" truevalue="--no-inferred" falsevalue="" checked="false" optional="true" label="Add the sequences of inferred alleles (INF) to the schema" help="Use this parameter if the schema is being accessed by multiple processes/users simultaneously." />
             <param argument="--prodigal-mode" type="select" optional="true" label="Prodigal Mode" help="&quot;single&quot; for finished genomes, reasonable quality draft genomes and big viruses. &quot;meta&quot; for metagenomes, low quality draft genomes, small viruses, and small plasmids">
diff --git a/tools/chewbbaca/ExtractCgMLST.xml b/tools/chewbbaca/ExtractCgMLST.xml
index 753859a6fe1..e59618e571b 100644
--- a/tools/chewbbaca/ExtractCgMLST.xml
+++ b/tools/chewbbaca/ExtractCgMLST.xml
@@ -23,7 +23,7 @@
         <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
         <section name="advanced" title="Advanced options">
             <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/>
-            <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values">
+            <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values as a space-separated list.">
                 <validator type="regex">[ .0-9]+</validator>
             </param>
             <param name="genes2remove" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove paralogous counts?" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process. --genes2remove"/>

From 1c51e770bde59b1b82f6f9a59df18de7ffe0a261 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 10 Apr 2024 16:24:40 +0200
Subject: [PATCH 79/97] update the name of test2 output

---
 tools/chewbbaca/AlleleCallEvaluator.xml          |  2 +-
 .../allelecallevaluator_report_annotate.html     | 16 ++++++++++++++++
 2 files changed, 17 insertions(+), 1 deletion(-)
 create mode 100644 tools/chewbbaca/test-data/allelecallevaluator_report_annotate.html

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index d1771b013fd..0b4f51cca85 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -76,7 +76,7 @@
             </param>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
             <param name="annotations" value="schema_seed_annotations.tsv"/>
-            <output name="html_file" file="allelecallevaluator_report.html" ftype="html" compare="sim_size">
+            <output name="html_file" file="allelecallevaluator_report_annotate.html" ftype="html" compare="sim_size">
             </output>
         </test>
     </tests>
diff --git a/tools/chewbbaca/test-data/allelecallevaluator_report_annotate.html b/tools/chewbbaca/test-data/allelecallevaluator_report_annotate.html
new file mode 100644
index 00000000000..fb8d807fbf4
--- /dev/null
+++ b/tools/chewbbaca/test-data/allelecallevaluator_report_annotate.html
@@ -0,0 +1,16 @@
+
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>AlleleCall Report - React Edition</title>
+</head>
+<body style="background-color: #f6f6f6">
+    <noscript> You need to enable JavaScript to run this app. </noscript>
+    <div id="root"></div>
+    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"], "loci_data": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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"GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265:0.000000000);\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>
+    <script src="./report_bundle.js"></script>
+</body>
+</html>
+

From 28219f5200a0ab283d7c5de2061f100a9c11faca Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 10 Apr 2024 17:30:48 +0200
Subject: [PATCH 80/97] update on 2nd test of AlleleCallEvaluator

---
 tools/chewbbaca/AlleleCallEvaluator.xml                   | 6 +++++-
 tools/chewbbaca/test-data/allelecallevaluator_report.html | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 0b4f51cca85..21be2494df7 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -76,7 +76,11 @@
             </param>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
             <param name="annotations" value="schema_seed_annotations.tsv"/>
-            <output name="html_file" file="allelecallevaluator_report_annotate.html" ftype="html" compare="sim_size">
+            <output name="html_file" file="allelecallevaluator_report_annotate.html" ftype="html">
+                <assert_contents>
+                    <has_text_matching expression="&quot;annotations&quot;"/>
+                    <has_text_matching expression="&quot;Uniprot_Name&quot;"/>
+                </assert_contents>
             </output>
         </test>
     </tests>
diff --git a/tools/chewbbaca/test-data/allelecallevaluator_report.html b/tools/chewbbaca/test-data/allelecallevaluator_report.html
index fb8d807fbf4..423fe059c6e 100644
--- a/tools/chewbbaca/test-data/allelecallevaluator_report.html
+++ b/tools/chewbbaca/test-data/allelecallevaluator_report.html
@@ -9,7 +9,7 @@
 <body style="background-color: #f6f6f6">
     <noscript> You need to enable JavaScript to run this app. </noscript>
     <div id="root"></div>
-    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", 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"", "", ""], ["GCA-000007265-protein20", "GCA_000007265", "AE009948.1", "30369", "31337", "20", "1", "Ribose-phosphate pyrophosphokinase 1", "http://purl.uniprot.org/uniprot/Q8E2H0", "", "", "", "", ""], ["GCA-000007265-protein57", "GCA_000007265", "AE009948.1", "73207", "74697", "57", "1", "Threonine synthase", "http://purl.uniprot.org/uniprot/A0A0E1EJC0", "", "", "", "", ""], ["GCA-000007265-protein42", "GCA_000007265", "AE009948.1", "55017", "55898", "42", "1", "N-acetylmannosamine kinase", "http://purl.uniprot.org/uniprot/A0A0E1EJA4", "", "", "", "", ""], ["GCA-000007265-protein14", "GCA_000007265", "AE009948.1", "13935", "15911", "14", "1", "ATP-dependent zinc metalloprotease FtsH", "http://purl.uniprot.org/uniprot/Q8E7Y0", "", "", "", "", ""], ["GCA-000007265-protein76", "GCA_000007265", "AE009948.1", "84290", "84646", "76", "1", "Large ribosomal subunit protein uL18", "http://purl.uniprot.org/uniprot/Q3K3V3", "", "", "", "", ""], ["GCA-000007265-protein98", "GCA_000007265", "AE009948.1", "102081", "102833", "98", "1", "Peptidase M15B domain-containing protein", "http://purl.uniprot.org/uniprot/Q8E7R1", "", "", "", "", ""], ["GCA-000007265-protein64", "GCA_000007265", "AE009948.1", "79220", "79498", "64", "1", "Small ribosomal subunit protein uS19", "http://purl.uniprot.org/uniprot/Q1JE54", "", "", "", "", ""], ["GCA-000007265-protein52", "GCA_000007265", "AE009948.1", "66381", "66818", "52", "1", "protein-tyrosine-phosphatase", "http://purl.uniprot.org/uniprot/A0A0E1EJB3", "", "", "", "", ""], ["GCA-000007265-protein10", "GCA_000007265", "AE009948.1", "10295", "10666", "10", "1", "Cell division protein DivIC", "http://purl.uniprot.org/uniprot/Q8E7Y5", "", "", "", "", ""]]}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", 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{"phylo_data": "(GCA_000007265:0.000000000);\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>
+    <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", 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["GCA-000007265-protein20", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein21", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein22", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein33", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein43", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein42", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein41", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein40", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein39", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein38", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein37", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein36", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein35", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein34", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein32", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein23", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein31", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein30", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein3", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein29", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein28", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein27", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein26", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein25", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein24", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein99", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein16", 3, 0, 1, 0.0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "annotations": [{"columns": []}, {"rows": []}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265:0.000000000);\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>
     <script src="./report_bundle.js"></script>
 </body>
 </html>

From 4b45c8fb8973e539e740846b73774e58183529c3 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Thu, 11 Apr 2024 11:29:03 +0200
Subject: [PATCH 81/97] Update tools/chewbbaca/CreateSchema.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/chewbbaca/CreateSchema.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 24b6c53a8a8..383fa09adc1 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -52,8 +52,8 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-        <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
-        <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip" compare="sim_size"/>
+            <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
+            <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>

From b669c997a38aa50bc70b517d7f3c8263132053b2 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 16:42:24 +0200
Subject: [PATCH 82/97] changed test of CreateSchema to check the archive
 members

---
 tools/chewbbaca/CreateSchema.xml | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index 383fa09adc1..e139fa89379 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -53,17 +53,33 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
-            <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed.zip" compare="sim_size"/>
+            <output name="schema">
+                <assert_contents>
+                    <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
+                    <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>
+                    <has_archive_member path="schema_seed/\.schema_config"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
             <param name="training_file" value="Streptococcus_agalactiae.trn"/>
-            <output name="schema" file="GCA_000007265.1_ASM726v1_schema_seed_trn.zip" compare="sim_size"/>
+            <output name="schema">
+                <assert_contents>
+                    <has_archive_member path="schema_seed/.*\.fasta" n="198"/>
+                    <has_archive_member path="schema_seed/short/.*\.fasta" n="99"/>
+                    <has_archive_member path="schema_seed/\.schema_config"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <param name="input_file" value="CDS_Str_agalactiae.fasta"/>
             <param name="cds_input" value="true"/>
-            <output name="schema" file="Str_agalactiae_cds.zip" compare="sim_size"/>
+            <output name="schema">
+                <assert_contents>
+                    <has_archive_member path="schema_seed/CDS-Str-agalactiae-protein1.fasta"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>

From 1772a319f3059ed3be1950175c819e600c067276 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 16:48:29 +0200
Subject: [PATCH 83/97] changed test of DownloadSchema to check the archive
 members

---
 tools/chewbbaca/DownloadSchema.xml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/tools/chewbbaca/DownloadSchema.xml b/tools/chewbbaca/DownloadSchema.xml
index eb1b1318978..2c1c7fc9bb5 100644
--- a/tools/chewbbaca/DownloadSchema.xml
+++ b/tools/chewbbaca/DownloadSchema.xml
@@ -46,6 +46,14 @@
                 <has_text text="Schema is now available at"/>
                 <has_text text="Finished at"/>
             </assert_stdout>
+            <output name="schema">
+                <assert_contents>
+                    <has_archive_member path="schema_seed/.*\.fasta" n="4446"/>
+                    <has_archive_member path="schema_seed/short/.*\.fasta" n="2223"/>
+                    <has_archive_member path="schema_seed/\.ns_config"/>
+                    <has_archive_member path="schema_seed/\.schema_config"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>

From 4be471103316f8affed13aeb0fb18d3daa4d6410 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 16:53:59 +0200
Subject: [PATCH 84/97] changed format=tsv to =tabular in CreateSchema

---
 tools/chewbbaca/CreateSchema.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/CreateSchema.xml b/tools/chewbbaca/CreateSchema.xml
index e139fa89379..df7bf2cb871 100644
--- a/tools/chewbbaca/CreateSchema.xml
+++ b/tools/chewbbaca/CreateSchema.xml
@@ -46,7 +46,7 @@
         <data format="txt" name="txt_file" from_work_dir="output/invalid_cds.txt" label="${tool.name} on ${on_string}: Invalid CDS">
             <filter>output['show_cds_invalid']</filter>
         </data>
-        <data format="tsv" name="tst_file" from_work_dir="output/cds_coordinates.tsv" label="${tool.name} on ${on_string}: CDS coordinates">
+        <data format="tabular" name="tsv_file" from_work_dir="output/cds_coordinates.tsv" label="${tool.name} on ${on_string}: CDS coordinates">
             <filter>output['show_cds_coord']</filter>
         </data>
     </outputs>

From a0e8b3112060daa631c5a3493608c3aca18dfd34 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 16:55:23 +0200
Subject: [PATCH 85/97] changed format=tsv to =tabular in JoinProfile

---
 tools/chewbbaca/JoinProfiles.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/JoinProfiles.xml b/tools/chewbbaca/JoinProfiles.xml
index 819d042bca1..2581eb6a4cb 100644
--- a/tools/chewbbaca/JoinProfiles.xml
+++ b/tools/chewbbaca/JoinProfiles.xml
@@ -15,7 +15,7 @@
         <param argument="--common" type="boolean" truevalue="--common" falsevalue="" checked="false" label="Common" optional="true" help="Create file with profiles for the set of common loci" />
     </inputs>
     <outputs>
-        <data format="tsv" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>
+        <data format="tabular" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>
     </outputs>
     <tests>
         <test>

From 0f0cc2d2f6674deb78e01d4e4d51409815e067e3 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 17:09:46 +0200
Subject: [PATCH 86/97] compare diff in JoinProfile

---
 tools/chewbbaca/JoinProfiles.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/JoinProfiles.xml b/tools/chewbbaca/JoinProfiles.xml
index 2581eb6a4cb..bb89b6d15ed 100644
--- a/tools/chewbbaca/JoinProfiles.xml
+++ b/tools/chewbbaca/JoinProfiles.xml
@@ -20,7 +20,7 @@
     <tests>
         <test>
             <param name="input1" value="results_alleles.tsv,results_alleles2.tsv"/>
-            <output name="JoinedProfile" file="JoinedProfile.tsv" compare="sim_size"/>
+            <output name="JoinedProfile" file="JoinedProfile.tsv" compare="diff"/>
         </test>
     </tests>
     <help>

From c50ca26bcd7affcb951f4c0be50d4f94e0661214 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 17:15:53 +0200
Subject: [PATCH 87/97] compare diff in AlleleCallEvaluator

---
 tools/chewbbaca/AlleleCallEvaluator.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/AlleleCallEvaluator.xml b/tools/chewbbaca/AlleleCallEvaluator.xml
index 21be2494df7..e93895a50d4 100644
--- a/tools/chewbbaca/AlleleCallEvaluator.xml
+++ b/tools/chewbbaca/AlleleCallEvaluator.xml
@@ -62,7 +62,7 @@
                 </collection>
             </param>
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
-            <output name="html_file" file="allelecallevaluator_report.html" ftype="html" compare="sim_size">
+            <output name="html_file" file="allelecallevaluator_report.html" ftype="html" compare="diff">
             </output>
         </test>
         <test expect_exit_code="0">

From 3a94dc707eec021e490428f8bd1637591db5132a Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 17:20:48 +0200
Subject: [PATCH 88/97] compare diff and assert_contents in NSSTATS

---
 tools/chewbbaca/NSStats.xml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index 85bfd297e36..e4301fdb4a0 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -32,7 +32,12 @@
     <tests>
         <test>
             <param name="mode" value="species" />
-            <output name="NSStats" file="NSStats.txt" compare="sim_size" />
+            <output name="NSStats" file="NSStats.txt" compare="diff">
+                <assert_contents>
+                    <has_text_matching expression="Streptococcus pyogenes"/>
+                    <has_text_matching expression="Clostridium neonatale"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>

From 72259d6c2f9efe072d6f7acddde7e2ef0af883e2 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 17:32:41 +0200
Subject: [PATCH 89/97] test checks archive members in PrepExternalSchema

---
 tools/chewbbaca/PrepExternalSchema.xml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/tools/chewbbaca/PrepExternalSchema.xml b/tools/chewbbaca/PrepExternalSchema.xml
index 102c1fadc4f..18234a1baf4 100644
--- a/tools/chewbbaca/PrepExternalSchema.xml
+++ b/tools/chewbbaca/PrepExternalSchema.xml
@@ -36,7 +36,13 @@
         <test expect_num_outputs="1">
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
             <param name="size_filter" value="false"/>
-            <output name="schema" file="GCA_000007265.1_ASM726v1_PExternalschema_seed.zip" compare="sim_size"/>
+            <output name="schema">
+                <assert_contents>
+                    <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
+                    <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>
+                    <has_archive_member path="schema_seed/\.schema_config"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>

From 52195a5dd9f8ab38563fe41deabf503d81cd006a Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 18:06:08 +0200
Subject: [PATCH 90/97] sim_size to diff in AlleleCall

---
 tools/chewbbaca/AlleleCall.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 483a8c0cb84..a2fad21cdee 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -109,8 +109,8 @@
             <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
             <param name="output_selector" value="output_unclassified,output_missing,hash_profile" />
             <output_collection name="allelecall_results" type="list">
-                <element name="cds_coordinates" file="cds_coordinates.tsv" compare="sim_size"/>
-                <element name="loci_summary_stats" file="loci_summary_stats.tsv" compare="sim_size"/>
+                <element name="cds_coordinates" file="cds_coordinates.tsv" compare="diff"/>
+                <element name="loci_summary_stats" file="loci_summary_stats.tsv" compare="diff"/>
                 <element name="paralogous_loci" ftype="tabular">
                     <assert_contents>
                         <has_text_matching expression="Genome.*Loci.*CDS"/>
@@ -122,14 +122,14 @@
                         <has_text_matching expression="GCA_000007265.*1"/>
                     </assert_contents>
                 </element>
-                <element name="results_alleles" file="results_alleles.tsv" compare="sim_size"/>
+                <element name="results_alleles" file="results_alleles.tsv" compare="diff"/>
                 <element name="results_alleles_hashed" ftype="tabular">
                     <assert_contents>
                         <has_text_matching expression="FILE.*GCA-000007265-protein1.*GCA-000007265-protein10.*GCA-000007265-protein100"/>
                         <has_text_matching expression="GCA_000007265.*308e7666834338d0530d925b2737f2c6.*4aece26d201d59a90947e3400c7abf3f.*ebea148832aa2ae2704d37ebd5123169"/>
                     </assert_contents>
                 </element>
-                <element name="results_statistics" file="results_statistics.tsv" compare="sim_size"/>
+                <element name="results_statistics" file="results_statistics.tsv" compare="diff"/>
             </output_collection>
             <output_collection name="allelcall_log" type="list">
                 <element name="logging_info" ftype="txt">

From 9224590bc777ebb8544cf37329a87934ac801151 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 18:09:04 +0200
Subject: [PATCH 91/97] deleted unnecessary test data

---
 ...0007265.1_ASM726v1_PExternalschema_seed.zip | Bin 115704 -> 0 bytes
 ...CA_000007265.1_ASM726v1_schema_seed_trn.zip | Bin 144041 -> 0 bytes
 .../chewbbaca/test-data/Str_agalactiae_cds.zip | Bin 2519 -> 0 bytes
 .../chewbbaca/test-data/allelecall_report.html |  16 ----------------
 .../test-data/allelecall_report_annot.html     |  16 ----------------
 tools/chewbbaca/test-data/cgMLST_MSA.fasta     |   2 --
 6 files changed, 34 deletions(-)
 delete mode 100644 tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_PExternalschema_seed.zip
 delete mode 100644 tools/chewbbaca/test-data/GCA_000007265.1_ASM726v1_schema_seed_trn.zip
 delete mode 100644 tools/chewbbaca/test-data/Str_agalactiae_cds.zip
 delete mode 100644 tools/chewbbaca/test-data/allelecall_report.html
 delete mode 100644 tools/chewbbaca/test-data/allelecall_report_annot.html
 delete mode 100644 tools/chewbbaca/test-data/cgMLST_MSA.fasta

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deleted file mode 100644
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-    <title>AlleleCall Report - React Edition</title>
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["GCA-000007265-protein47", "GCA_000007265", "AE009948.1", "60012", "61103", "47", "1", "N5-carboxyaminoimidazole ribonucleotide synthase", "http://purl.uniprot.org/uniprot/A0A0E1EJA7", "", "", "", "", ""], ["GCA-000007265-protein99", "GCA_000007265", "AE009948.1", "102830", "103405", "99", "1", "Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain-containing protein", "http://purl.uniprot.org/uniprot/Q8E7R0", "", "", "", "", ""], ["GCA-000007265-protein102", "GCA_000007265", "AE009948.1", "105338", "107167", "102", "1", "Chaperone protein DnaK", "http://purl.uniprot.org/uniprot/P0A3J2", "", "", "", "", ""], ["GCA-000007265-protein96", "GCA_000007265", "AE009948.1", "100791", "101270", "96", "1", "Competence-specific sigma factor ComX", "http://purl.uniprot.org/uniprot/Q8E7R3", "", "", "", "", ""], ["GCA-000007265-protein66", "GCA_000007265", "AE009948.1", "79871", "80524", "66", "1", "Small ribosomal subunit protein uS3", "http://purl.uniprot.org/uniprot/A2RC20", "", "", 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{"phylo_data": "(GCA_000007265:0.000000000);\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>
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diff --git a/tools/chewbbaca/test-data/cgMLST_MSA.fasta b/tools/chewbbaca/test-data/cgMLST_MSA.fasta
deleted file mode 100644
index cb1a4d92330..00000000000
--- a/tools/chewbbaca/test-data/cgMLST_MSA.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->GCA_000007265
-MVQYNNNYPQDNKEEAMTENEQLFWNRVLELSRSQIAPAAYEFFVLEARLLKIEHQTAVITLDNIEMKKLFWEQNLGPVILTAGFEIFNAEITANYVSNDLHLQETSFSNYQQSSNEVNTLPIRKIDSNLKEKYTFANFVQGDENRWAVSASIAVADSPGTTYNPLFIWGGPGLGKTHLLNAIGNQVLRDNPNARVLYITAENFINEFVSHIRLDSMEELKEKFRNLDLLLIDDIQSLAKKTLGGTQEEFFNTFNALHTNDKQIVLTSDRNPNQLNDLEERLVTRFSWGLPVNITPPDFETRVAILTNKIQEYPYDFPQDTIEYLAGEFDSNVRELEGALKNISLVADFKHAKTITVDIAAEAIRARKNDGPIVTVIPIEEIQIQVGKFYGVTVKEIKATKRTQDIVLARQVAMYLAREMTDNSLPKIGKEFGGRDHSTVLHAYNKIKNMVAQDDNLRIEIETIKNKIRMRYSKEIIQLAIPAMIENILQMLMGVVDNYLVAQLGVVAVSGVSVANNIITIYQAIFIALGASIASLLAKSLAGSKKDDAISVCSQAIFLTLLIGAVLGIISIVFGQTFFKLLGTTKSVAQVGGLYLAIVGGGVVTLGMLTTLGSFLRVQGQPRLPMYVSIFVNFLNAVLSGFAIFEWRYGLVGVAVSTLIARLIGICILAKYLPIKKIIKRMTWKISAQIWNLALPSAGERLMMRAGDVVIVAIVVQLGTNVVAGNAIGETLTQFNYMPGLGIATATIILTAKYVGQKNRESIEETIQSSYYIGLVLMILISSFMLLAGKPLTQLFTNNPSAIKGSLIVILLSFVGVPATIGTLVYTAAWQGLGNAKLPFYTTTIGMWLIRVVLGYLLGIVFELGLLGVWMATIADNIFRWLFLKVHYHRYIQKMMLVPKRVKHRREFRGKMRGEAKGGKEVSFGEYGLQATTSHWITNRQIEAARIAMTRYMKRGGKVWIKIFPHKSYTAKAIGVRMGSGKGAPEGWVAPVKRGKVMFEIAGVSEEVAREALRLASHKLPVKCKFVKREAEMGQKVHPIGMRVGIIRDWDAKWYAEKEYADYLHEDLAIRKFINKELADASVSTIEIERAVNKVIVSLHTAKPGMVIGKGGANVDALRGQLNKLTGKQVHINIIEIKQPDLDAHLVGENIARQLEQRVAFRRAQKQAIQRTMRAGAKGIKTQVSGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGEVLPARKNTKGGKMAEITSAKAMARTVRVSPRKTRLVLDLIRGKNVADAIAILKFTPNKAARVIEKTLNSAIANAENNFGLEKANLVVSETFANEGPTMKRFRPRAKGSASPINKRTTHVTVVVSEKMGRSLKKGPFVDEHLMKKVEAQANDEKKKVIKTWSRRSTIFPSFIGYTIAVYDGRKHVPVYIQEDMVGHKLGEFAPTRTYKGHAADDKKTRRMGIKVYKPTTNGRRNMTSLDFAEITTNTPEKSLLVSLKNKAGRNNNGRITVRHQGGGHKRHYRLIDFKRNKDGVEAVVKTIEYDPNRTANIALVHYTDGVKAYILAPKGLEVGQRIISGPEADIKVGNALPLANIPVGTVIHNIELQPGKGAELIRAAGASAQVLGQEGKYVLVRLQSGEVRMILGTCRATIGTVGNEQQSLVNIGKAGRNRWKGVRPTVRGSVMNPNDHPHGGGEGKAPVGRKAPSTPWGKPALGLKTRNKKAKSDKLIVRRRNQKMNLYDVIKKPVITEKSMVALEAGKYTFEVDTRAHKLLIKQAVEAAFDGVKVASVNTVTVKPKAKRVGRYTGFTSKTKKAIITLTADSKAIELFAAEAEMANVKLFDQTGKEVSSVELNEAIFGIEPNESVVFDVVISQRASLRQGTHAVKNRSAVSGGGRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYGYKLPQKVRRLALKSVYSAKVAEDKFVAVENLSFAAPKTAEFASVLSALSIDSKVLVILEEGNEFAALSARNLPNVTVATATTASVLDIVNADKLLVTKEAISTIEGVLAMTKGILGKKVGMTQIFTESGEFIPVTVIEATPNVVLQVKTVETDGYEAVQVGFDDKREVLSNKPAKGHVAKANTAPKRFIREFKNIEGLEVGAELSVEQFEAGDVVDVTGTSKGKGFQGVIKRHGQSRGPMAHGSRYHRRPGSMGPVAPNRVFKNKRLAGRMGGNRVTVQNLEIVQVIPEKNVVLIKGNVPGAKKSLITIKSAVKAAKMALTAGIVGLPNVGKSTLFNAITKAGAEAANYPFATIDPNVGMVEVPDERLQKLTELITPKKTVPTTFEFTDIAGIVKGASKGEGLGNKFLANIREVDAIVHVVRAFDDENVMREQGREDAFVDPIADIDTINLELILADLESINKRYARVEKMARTQKDKESVAEFNVLQKIKPVLEDGKSARTIEFTEEEAKVVKGLFLLTTKPVLYVANVDEDKVADPDDIDYVNQIRAFAETENAEVVVISARAEEEISELDDEDKLEFLEAIGLTESGVDKLTRAAYHLLGLGTYFTAGEKEVRAWTFKRGIKAPQAASIIHSDFERGFIRAVTMSYDDLIQYGSEKAVKEAGRLREEGKEYIVQDGDIMEFRFNVMANKKIRIRLKAYEHRTLDTAAEKIVETATRTGATVAGPVPLPTERSLYTIIRATHKYKDSREQFEMRTHKRLVDIINPTQKTVDALMKLDLPSGVNVEIKLMAIVYQSTRDASNKVTASQAILKGLADDGGLFTPITFPKVDLDFTKLKDASYQEVAKLVLSAFFDDFTEQELDYCISQAYDTKFDTTEIAPIVKIGDRYHLELFHGPTIAFKDMALSILPYLLTTAAKKQGVDNKIVILTATSGDTGKAAMAGFADVPGTEIIVFYPKNGVSYIQELQMITQAGQNTHVVAIEGNFDDAQTSVKEMFNNSLLRLKLSQQHMQLSSANSMNIGRLVPQIVYYIYAYAQLVKSKEISIGQPINFSVPTGNFGNILAAYYASQIGLPVTKLICASNDNNVLTDFFKTQTYDKNREFKVTSSPSMDILVSSNLERLIFHLLGDDAETTKKLMEDLVTTGEYALEARQANILESFVAGFATEQFVELDIKHLFDQYQYIEDPHTAVASAVYQAYQTETKDQTPAVIVSTASPYKFPCVVTKAITNKEEIQDFAAISILNDLSGVSLPKAVTDLQKAEVIHRTVVPTSNMRETVEECLGLKQMERNQRKTLYGRVVSDKMDKTITVVVETKRNHPVYGKRINYSKKYKAHDENNVAKEGDIVRIMETRPLSATKRFRLVEVVEKAVIIMKAVVVNQASTGVEVVEHDLPKVGHGEALVKVEYCGVCHTDLHVAHGDFGQVPGRILGHEGIGIVEEIGEGVTSLRVGDRVSIAWFFEGCGHCEYCTTGRETLCRSVKNAGYSVDGGMSEYAIVTADYAVKVPEGLDPAQASSITCAGVTTYKAIKEAGAAPGQWIAVYGAGGLGNLAVQYAKKVFNAHVVAVDINADKLQLAKEVGADLTVNGKEIKDVAAYIQEKTGGCHGVVVTAVSKVAFNQAIDSVRAGGTVVAVGLPSEYMELSIVKTVLDGIRVVGSLVGTRKDLEEAFAFGAEGLVVPVVEKVPVDTAPQVFDEMERGLIQGRKVLDFTKMTEKTKAVETTDVALAIDTLVQNGLKALDEMRQLNQEQVDYIVAKASVAALDAHGELALHAVEETGRGVFEDKATKNLFACEHVVNNMRHTKTVGVIEEDDVTGLTLIAEPVGVVCGITPTTNPTSTAIFKSLISLKTRNPIIFAFHPSAQESSAHAARIVRDAAIAAGAPENCVQWIEQPSIDATNALMNHDGIATILATGGNAMVKAAYSCGKPALGVGAGNVPAYVEKSANIRQAAHDIVMSKSFDNGMVCASEQAVIIDKEIYKEFVEEFKSYHTYFVNKKEKALLEEFCFGAKANSKNCAGAKLNPNIVGKSAVWIAEQAGFTVPEGTNILAAECTEVSEKEPLTREKLSPVIAVLKAESTEDGVEKARQMVEFNGLGHSAAIHTKDADLAREFGTRIRAIRVIWNSPSTFGGIGDVYNAFLPSLTLGCGSYGRNSVGDNVSAINLLNIKKVGRRRNNMQWFKVPSKTYFERDSIQYLQKCRDVERVMIVTDHAMVELGFLDRIIEQLDLRRNKVVYQIFAEVEPDPDITTVMKGTDLMRTFKPDTIIALGGGSPMDAAKVMWLFYEQPEVDFHDLVQKFMDIRKRAFKFPELGKKTKFVAIPTTSGTGSEVTPFAVISDKANNRKYPIADYSLTPTVAIVDPALVMTVPGFIAADTGMDVLTHATEAYVSQMANDYTDGLALQAIKIVFDYLERSVKDADFEAREKMHNASTMAGMAFANAFLGISHSMAHKIGAQFHTVHGRTNAILLPYVIRYNGTRPAKTATWPKYNYYRADEKYQDIAKLLGLPAATPEEAVESYAKAVYDLGTRLGIKMNFRDQGIDEKEWKEKSRELAFLAYEDQCSPANPRLPMVDHMQEIIEDAYYGYEERPGRRKMRIKWFSLVRITGLLLVLLYHFFKNSFPGGFVGVDIFFTFSGFLITALLIDEFSKTKKIDFVSFCRRRFYRIFPPLVLMVLVTIPFVFLVKSDFRASIGSQIMTALGFTSNFYEILTGGNYESQFIPHLFVHTWSLSIEVHFYVLWGLTVWLLSKRSKDQKQLRGTLFLISMGIFGVSFLTMFVRAFFVDNFSTIYFSTLSHIFPFFLGAMVATISGIREITGRFKKNIKNLTLKHNLIMMGSAFAGLMILTFALDFDNRLTYLFGFVLSSIFASVMIYNARILHEHTPDISEPFVITYLADISYGMYLFHWPFYIIFSRLSPNWIAVILTVVLSAVFSTLSFYIIEPFILGRKPKFLDYEFDLLPYKKWLFSIGGVLTLITVVTMLTAPSIGSFETELLQNSLQQARTNTNRTHTLAAGDAGALSDVTVIGDSVALRSSAAFNKLLPEVQLDAAVSRNFSKSFDIFENRIQNKALSKIVVLAVGVNSLDNYKTDLSQFIKSLPKGHRLIIVTPYNAKNMSQVTTVRDYELSLMKKYNYITVADWYKVATEHPEIWGNTDGVHYSDSDTTGADLYVSNVKKAIQKSAQRAAKMKNFKITRTHLEILSLIIIVVFGLSVFTLTTSSQGVFSYDGGKIKYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHGWSYTGDFKKGQPDGQGRLNAKNKKVYKGTFKQGIYQKMKKVCFVCLGNICRSPMAEFVMANLDKEDSLLVESRATSTWEHGNPIHRGTQAILQRYQIPYINDKGSQPISKDDLAYFDYIIGMDEQNVKDLKALSQGTYDDKISLFCDGGVPDPWYTGDFEETYRLVNDGCKQWLTLINNSRDMTRFLDSDAMGDEELVERTLRPQYLREYIGQDKVKDQLKIFIEAAKLRDESLDHVLLFGPPGLGKTTMAFVIANELGVNLKQTSGPAIEKSGDLVAILNDLEPGDVLFIDEIHRMPMAVEEVLYSAMEDFYIDIMIGAGETSRSVHLDLPPFTLIGATTRAGMLSNPLRARFGITGHMEYYEENDLTEIIERTADIFEMKITYEAASELARRSRGTPRIANRLLKRVRDYAQIMGDGLIDDNITDKALTMLDVDHEGLDYVDQKILRTMIEMYNGGPVGLGTLSVNIAEERDTVEDMYEPYLIQKGFIMRTRTGRVATVKAYEHLGYQRFDKMLKHFGSKVRNLRVTRNITREDFCGDETELSVRQLARIESGQSIPNLTKAHYIAKQLNVKLDILTGGESLELPKRYKELKYLILRIPTYADAERLKLRECQFDHIFEEFYDNLPEDECLAIDSLQAKFEVYQTGDINFGVEVLCECFDKVKYKEKYTLNDLIIIDLFLTCAVVSKFNNRAFTKEVFQTICKTLISQNHKLTAEDLFWFNHVLLNCVFVGLCLNSEECLAEMLEVSRQTMVSTHDFHKMPLYFMYQWKYFITIDNDIKSAENAYQQSIMFSKMIDDKHLIKKLELEWQEDITGHMDNLIRLAEIFDVSLDEHVLAKTNEVKVERIYENKPLDLRKYNKIYWFIFRNIIRSLLIILAILTFLMIERYSRPEMAAIWTEENKYRAWLEVEILADEAWAELGEIPKEDVAKIREKADFDIDRILEIEQDTRHDVVAFTRAVSETLGEERKWVHYGLTSTDVVDTAYGYLYKQANDIIRRDLENFTNIVADKAKEHKFTIMMGRTHGVHAEPTTFGLKLATWYSEMKRNIERFEHAAAGVEAGKISGAVGNFANIPPFVEQYVCDKLGIRPQEISTQVLPRDLHAEYFAVLASIATSIERMATEIRGLQKSEQREVEEFFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGHMVTAYENVALWHERDISHSSAERIITPDTTILIDYMLNRFGNIVKNLTVFPENMMRNMESTFGLIYSQRVMLKLIEKGMTREEAYDLVQPKTAYSWDNQVDFKPLLEEDTKVTSCLTQEEIDELFNPIYYTKRVDDIFERLGLEKMNRIINRDILPRISKISKNNKEKDLLSIAYITWLIFIIFALGVVTVNDLKPMFNQLIVNLLNIYYYMEAFILGMDSYLQYNLPYSFDFWSIFVEAINLFVKVFLIAFIPSVIRKVLKKESFFNEVVILLGAIVTIIVSFHLYLEILIVVGLILLLIAFVSIGKNRVYNFVQNLNYFEEVIWNYFEENPVKIKEKSLIIKFLLTISFVFVIDFAMVRLLNFNIKFSTILACSAILLAWLYQNKSVTEPFLLKKLVIYFIFFIATLIGNLKNELSILETPLLFISIFFTMDRIIALSKEMRDLIISKSILFYYDHENIKPSILLSEIKEIKYLENVDIGELELVRQMVIRLRLELEEEFLILSDIYMKNGYEKYIQFVQGNVYFINLELDKIPNYTNLKLILESIFDHNNQKIFIPKLYEEYIYILISLGEVEKAKEILKEVSDYLTEESLNYFEKEYDKAKGSNMKLQEIKDFVKELRGLSQEELAKKENELKKELFDLRFQAAAGQLEKTARLDEVKKQIARVKTVQSEMKMVKMIVGLGNPGSKYNDTKHNIGFMAVDRIVKDLDVNFTEDKNFKAEIGSDFINGEKIYFIKPTTFMNNSGIAVKALLTYYNISIKDMIIIYDDLDMEVGKIRFRQKGSAGGHNGIKSIIAHLGTQEFDRIKVGIGRPNGRMTVINHVLGKFDKNDEIMILNTLDKVDNAVNYYLQTNDFQKTMQKYNGLKMSKPNVVQLNNQYINDENLKKRYEAEELRRKNRLMGWVLIFVMLLFILPTYNLVKSYRTLQERRQEVVKLTKDYQTLTNRTENQKLLAKQLKNPDYVQKYARAKYYFSKTGEMIYPLPDLLPKMARIAGVDIPNDKRVVISLTYVYGIGLSTSKKILAAAGISEDIRVKDLTPDQEDAIRREVDAIKVEGDLRREVNLNIKRLMEIGSYRGIRHRRGLPVRGQNTKNNARTRKGKAVAIAGKKKMKKNKIIRFSLVGVLLAILCFSLFALLKPNSQQSSSQKLRNEDIKKISSQKRNKKLQLPAVSSKDWNLILVNRDHKHEELSPDVVPVENIYLDKRITKQATQFLEAARAIDSREHLISGYRSVAYQEKLFNSYVTQEMTSNPNLTRGQAEKLVKTYSQPAGASEHQTGLAMDMSTVDSLNESDPRVVSQLKKIAPQYGFVLRFPDGKTAETGVGYEDWHYRYVGVESAKYMAKHHLTLEEYITLLKENNQMSKVRLYIARHGKTMFNTIGRAQGWSDTPLTTFGELGIKELGLGLKASNISFKEAFSSDSGRTLQTMEIILREVQQENIPYTRDKRIREWCFGSLDGGYDGDLFNGVLPRVSNGDMSHLTHEEIANLICQVDTAGWAEPWAILSNRILSGFTAIAKKIEDIGGGNAIVVSHGMTIATFLWLIDHSTPRSLGLDNGSVSVVDFEDGTFSIQSIGDMSYREKGREILEKTLQMRDFEELFDKVKPIVMKLRRNYFVQLWEYDDWIQEGRIVLFRLLEEHPYLLDNESKLFIYFKTKFSNYLNDVLRHQDCQKRQFNKMPYEEISEVSHYVKSKGLVLDDYIAYRDTLTKVEETLSDIDKEKFEKLISGERFAGKKQFIRDIQPFFNAFKADMKMTVYFDGNFWLGLIEYDDDGDYKVFRYFFGKEPKDDDVFNFINHKLNDLIKKYEFVKTDISLKRTNEHKKSPKRMQREINREKRKPVVSTKAQLAMKTIHMSIKNERQLSQKCKKNELRKHRYQLKQEKRYQKKKGHMTKIYHMILCNSDIMKILAIIKSLPLNDCWLCAGTLRNFVWNKLSGINETLTSDIDVVFFDKNISYEETVVLEQQLKDNYPQYDWELKNEFYMNTHSPNTPKYTSSKDAISKFPEKCTAVGARLDDRNQLELYLPYGEEEILNFIVSPTPYFEEDLLRYNVYLKRVDKKKWNNIWPRLTIIKKMINKPLLRKNKNNNIVIPPNTSNKLTFSSLKISSLFHMYKVIKRILKTMYQYMTLDTRLKYFNFYSPFKDVFENTIMEHTYSKILNMRLDKYLKVSRIIKRRPVAKEVADKGRVKVNGVLAKSSTDLKLNDQVEIRFGNKLLTVKVLEMKDSTKKEDAIKMYEIINETRIETDEQAMAYRKLGRTSSQRKAMLRDLTTDLLINESIVTTEARAKEIRKTVEKMITLGKRGDLHARRQAAAYVRNEIASENYDEASDKYTSTTALQKLFDDIAPRYAERNGGYTRILKTEPRRGDAAPMAIIELVMIEFEKPIITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKIKLADLGLGLKNDKMAKPTRKRRVKKNIESGVAHIHATFNNTIVMITDVHGNALAWSSAGALGFKGSRKSTPFAAQMAAEAAAKSAQEHGLKTVEVTVKGPGSGRESAIRALAAAGLEVTAIRDVTPVPHNGARPPKRRRVMAKEDVIEIEGKVVETMPNAMFTVELENGHQILATVSGKIRKNYIRILVGDRVTVEMSPYDLTRGRITYRFKMIQQETRLKVADNSGAREILTIKVLGGSGRKFANIGDVIVASVKQATPGGAVKKGDVVKAVIVRTKTGARRPDGSYIKFDDNAAVIIRDDKTPRGTRIFGPVARELREGGYMKIVSLAPEVLMNLLIMGLPGAGKGTQAAKIVEEFGVAHISTGDMFRAAMANQTEMGRLAKSYIDKGELVPDEVTNGIVKERLAEDDIAEKGFLLDGYPRTIEQAHALDATLEELGLRLDGVINIKVDPSCLIERLSGRIINRKTGETFHKVFNPPVDYKEEDYYQREDDKPETVKRRLDVNIAQGEPILEHYRKLGLVTDIEGNQEITEVFADVEKALLELKMFLKLLRDALKVKMVRNKILFTIFILLVFRIGTHITVPGINVKSLEQMGELPFLNMLNLVSGNAMRNFSVFSMGVSPYITASIVVQLLQMDILPKFVEWGKQGEVGRRKLNQATRYISLFLAFVQSIGITAGFNTLSSVALVKTPNVQTYLLIGAILTTGSMVVTWLGEQITDKGFGNGVSMIIFAGIISSIPSAITTIYEDFFVNVRSSAITNSYIFVGILIVAVLAIVFFTTFIQQAEYKIPIQYTKLVQGAPTSSYLPLKVNPAGVIPVIFASSITTIPSTIIPFFQNGKEIPWLTKLQELLNYQTPVGMIIYAILIILFSFFYTFVQVNPEKTAENLQKNSSYIPSIRPGRETEEYMSSLLKKLATIGSVFLAFISLLPIIAQQALHLSSSIALGGTSLLILIATGIEGMKQLEGYLLKRRYVGFMNTTEMNIIELFSQNKVVRTWHSGLVTNSRQLVMGFSGASKAIAIASAYEKLSKKIMVVTATQTDSDKLSSDISSLIGEDNVYQFFADDVPAAEFIFSSLDKSISRLSALRFLKDPEKNGVLITSISGLRLLLPNPEVFSKSQYKFEIGQECYLDKLCKNLVNLGYQKVSQVFSPGEFSQRGDILDIFEMTQEYPYRLEFFGDEIDGIRQFDIDTQKSLKQLESVQISPADDIILQDADFERAKKKLEGYLVTASEVQRTYLSEVLSTTENHFKHSDIRRFLSIFYEKEWGILDYIPEGTPLFVDDFQKIVDRNAKLDLEIASLLTEDLQQGKSHSSLNYFSDPYKQLRQYQPATFFSNFHKGLGNLKFDKLHHFTQYGMQEFFNQFPLLVDEINRYKKSGATVLLQVDSQKGLNLLQENLKEYGLDLIISDKNDIVQKESQLIVGHLSNGFYFADEKIVLITEREIYHRRVKRKIRRSNISNAERLKDYNELSVGDYVVHNVHGVGKFLGIETIEIQGIHRDYLTIQYQNADRISIPVEQIELLTKYVSADGKEPKINTLNDGRFKKAKQRVAKQVEDIADDLLKLYAERSQLQGFAFSPDDNMQNDFDNDFAYVETEDQLRSIKEIKQDMEGNRPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVVVLVPTTVLAQQHFENFKERFSNYPVTVDVLSRFRSKKEQTDTLKRLSKGQVDIIIGTHRLLSQDVVFSDLGLIVIDEEQRFGVKHKEKLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLETNPGLVREAIIREIDRGGQVFYVYNKVDTIDQKVSELQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNTLFVENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEISEKRLDAIKGFTELGSGFKIAMRDLSIRGAGNILGASQSGFIDSVGFEMYSQLLEQAIATKQGKSLIRQKGNAELALQIDAYLPAEYISDERQKIEIYKRIRELETRADYEALQDELIDRFGEYPDQVAYLLEIGLLKAYLDLAFTELVERKGNEISILFEKASLKYFLTQDYFEALSKTQLKARISETNGKMEVVFNIKHKKNYEIIEELLKFAECFIEIKSRKPVEEMKLHELKPAEGSRKVRNRVGRGTSSGNGKTSGRGQKGQKARSGGGVRLGFEGGQTPLFRRMPKRGFSNINAKEYALVNLDQLNVFEDGTEVTPVVLKEAGIVRAEKSGVKILGNGELTKKLSVKAAKFSKSAEAAITAKGGSIEVIMAFKDNAVELEERVVAINRVTKVVKGGRRLRFAALVVVGDRNGRVGFGTGKAQEVPEAIRKAVEAAKKNMVEVPMVGTTIPHEVRSEFGGAKVLLKPAVEGAGVAAGGAVRAVIELAGVADITSKSLGSNTPINIVRATVEGLKQLKRAEEVAALRGISVSDLAMISKPDKNKIRQKRHRRVRGKLSGTADRPRLNIFRSNTGIYAQVIDDVAGVTLASASTLDKEVSNGTKTEQAVVVGKLVAERAVAKGISEVVFDRGGYLYHGRVKALADSARENGLKFMSRIGNKVITLPAGVEIINKDNVVTVKGPKGQLTREFNKNIGITVEGTEVTVTRPNDSKEMKTIHGTTRANLNNMVVGVSEGFKKALEMRGVGYRAQLQGSKLVLSVGKSHQDEVEAPEGVTFEVPTPTTINVIGINKESVGQTAAYVRSLRSPEPYKGKGIRYVGEFVRRKEGKTGKMVMTDPIADFLTRIRNANQAKHEVLEVPASNIKKGIADILKREGFVKNVEVIEDDKQGIIRVFLKYGQNGERVITNLKRISKPGLRVYTKHEDMPKVLNGLGIAIVSTSEGLLTDKEARQKNIGGEVLAYIWMANRLKEKYTNEVVPALTEKFNYSSVMAVPKVEKIVLNMGVGDAVSNAKNLEKAAAELALISGQKPLITKAKKSIAGFRLREGVAIGAKVTLRGERMYEFLDKLVSVSLPRVRDFHGVPTKSFDGRGNYTLGVKEQLIFPEINFDDVDKVRGLDIVIVTTANTDEESRELLKGLGMPFAKMFVKKGDKVRVIAGKDKGTEAVVLKALPKVNKVVVEGVALIKKHQKPNNENPQGAIVEKEAPIHVSNVQVLDKNGVAGRVGYKVVDGKKVRYNKKSGEVLDMNSFKTIGIIGGGQLGQMMAIAAIYMGHKVITLDPASDCPASRVSEVIVAPYDDVEALGTLAARCDVLTYEFENVDADGLDAVVSAGQLPQGTDLLRISQNRIFEKDFLANKAGVTVAPYKVVTSSLDLEGLDLTKTYVLKTATGGYDGHGQKVIRSAEDLPEAQQLANSAQCVLEEFVNFDLEISVIVSGNGQDVTVFPVQENIHRNNILSKTIVPARISDQLADKAKEMAVQIAKKLQLSGTLCVEMFATADDIIVNEIAPRPHNSGHYSIEACDFSQFDTHILGVLGAPLPPIKLHAPAVMFNVLGQHVQQAIDHVAQNPSAHLHMYGKLEAKHNRKMGHVTVFSDVPDEVEEFEERMDFMQKTAEVLDNFGIAYEKKVVSAHRTPDLMFKHAEEARGRGIKIIIAGAGGAAHLPGMVAAKTTLPVIGVPVKSRALSGLDSLYSIVQMPGGVPVATMAIGEAGATNAALTALRILSIEDQNLADALAHFHEEQGKIAEESSNELIMKLLVVGSGGREHAIAKKLLASKDVDQVFVAPGNDGMTLDGLDLVNIGISEHSRLIDFVKENEIAWTLIGPDDALAAGIVDGFNSAGLRAFGPTKAAAELEWSKDFAKEIMVKYNVPTAAYGTFSDFEKAKAYIEEQGAPIVVKADGLALGKGVVVAETVEQAVEAAQEMLLDNKFGDSGARVVIEEFLDGEEFSLFAFANGDKFYIMPTAQDHKRAYDGDKGLNTGGMGAYAPVPHLPQSVVDTAVETIVKPVLEGMIAEGRPYLGVLYAGLILTADGPKVIEFNSRFGDPETQIILPRLTSDFAQNIDDIMMGIEPYITWQKDGVTLGVVVASEGYPLDYEKGVPLPEKTDGDIITYYAGAKFAENSKALLSNGGRVYMLVTTEDSVKAGQDKIYTQLAQQDTTGLFYRNDIGSKAIKEMTIYDQIESALDLMTDLEREIACYFMGQPISKDALASTIVTKQLHISQAALTRFAKKCGFKGYREFVFEYLKSHETISQQLYGLQNDNTKKVFMNYQEMISKSADIIDEEQLLEVSHMIEQADRVYFYGKGSSSLVAKEFKIRLMRLGVICEALDDTDSFSWTNSIVNDRCLVIAFSLSGNTNSVIGALKIASCHGAKTVLFTKQPHTIDYAFDKIIQVASARHLDYGNRISPQIPMLIMVDIIYAQFLDINKIEKERIFRETIIQRMIHFSINKNFFLHALTVTKRAISHKNAIPILSTVKIEVTRDAIILTGSNGQISIENTIPASNENAGLLVTNPGSILLEAGFFINIISSLPDVTLEFTEIEQHQIVLTSGKSEITLKGKDVDQYPRLQEMTTDTPLTLETKLLKSIINETAFAASQQESRPILTGVHLVISQNKYFKAVATDSHRMSQRTFQLEKSANNFDLVVPSKSLREFSAVFTDDIETVEVFFSDSQMLFRSENISFYTRLLEGNYPDTDRLLTNQFETEIIFNTNALRHAMERAYLISNATQNGTVRLEIQNETVSAHVNSPEVGKVNEELDTVSLKGDSLNISFNPTYLIESLKAVKSETVTIRFISPVRPFTLTPGEDTEDFIQLITPVRTNMKKRILSAVLVSGVTLGTAAVTVNADDFDSKIAATDSVINTLSGQQAAAQNQVTAIKGQVGALESQQSELEAQNAQLEAVSQQLGQEIQTLSNKIVARNESLKKQVRSAQKGNLTNYINTILNSKSVSDAVNRVVAIREVVSANEKMLAQQEADKAALEAKQIENQNAINTVAANKQAIENNKAALATQRAQLEAAQLELSAQLTTVQNEKASLIQAKAQAEEAARKAAEAQAAAEAKAQAEAKAQAESVAKAQAAAQVESATAPTETVQTQPRTEIKPSNLTATSSATTVATTTATATNEPKVTQPSVVTKAVEAPKAVVSSTPRAVSKPVVRSYDSSNTYPMGQCTWGAKSMASWVGNYWGNANQWGASARAAGYSVGTTPRVGAVAVWPYDGGGYGHVAVVTSVANNSSIQVMESNYAGNMSIGNYRGSFNPSASGSVYYIYPNMKNNKNNGFLKNSFIYILLIIAVITTFQYYLKGTSSQNQQISYTKLVKQLKAGEIKSISYQPSGGVVEVSGTYKKAKTIKSANSFTFLGGSVATKVTGFNSVILPNDSSIKSLVSAAEENNTNIQVKHESSSGTWISYIASFLPLVIMIGFFMMMMNQGGGGGARGAMSFGKNKARSSSKDEVKVRFSDVAGAEEEKQELIEVVDFLKDPKRYKSLGARIPAGVLLEGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAERAIIFIDEIDAVGRRRGAGMGGGNDEREQTLNQLLIEMDGFEGNESIIVIAATNRSDVLDPALLRPGRFDRKVLVGQPDVKGREAILRVHAKNKPLADNVDLKVVAQQTPGFVGADLENVLNEAALVAARRNKKVIDASDIDEAEDRVIAGPSKKDRTISERERAMVAYHEAGHTIVGLILSNARVVHKVTIVPRGRAGGYMIALPKEDQMLLSKDDMKEQLAGLMGGRVAEEIIFNAQTTGASNDFEQATAMARAMVTEYGMSEKLGPVQYEGNHAMMAGQMSPEKSYSAQTAQLIDDEVRHLLNEARNKAADIINENRDTHKLIAEALLKYETLDAAQIKSIFETGKMPETENDEDKARALSYDEIKEKMQEEDKKMLENDIKKVLYSEEDIILKTKELGAKLTADYAGKNPLLVGVLKGSVPFMAELLKHIDTHVEIDFMVVSSYHGGTTSSGEVKILKDVDTNIEGRDVIFIEDIIDTGRTLKYLRDMFKYRQANSVKVATLFDKPEGRLVDIDADYVCYDIPNEFIVGFGLDYAENYRNLPYVGVLKEEIYSKMYNTILKDTLSKGLFTAHQKVLIAVSGGIDSINLLQFLYQYQKELSISIGIAHINHGQRKESEKEEEYIRQWGQIHDVPVFISYFQGIFSEDRARNHRYNFFSKVMREEGYTALVTAHHADDQAETVFMRILRGSRLRYLSGIKQVSAFANGQLIRPFLPYKKELLPNIFHFEDASNASSDYLRNRIRNVYFPALERENNQLKDSLITLSEETECLFTALTDLTRSIEVTNCYDFLRQTHSVQEFLLQDYISKFPDLQVSKEQFRVILKLIRTKANIDYTIKSGYFLHKDYESFHITKIHPKTDSFKVEKRLELHNIQIFSQYLFSYGKFISQADITIPIYDTSPIILRRRKEGDRIFLGNHTKKIRRLFIDEKITLKEREEAVIGEQNKELIFVIVAGRTYLRKPSEHDIMKGKLYIENLEKRMSKVRGFELVSQFSNKELLPKRETAHAAGYDLKVAKKTVIEPGEITLVPTGIKAYMQPGEVLYLYDRSSNPRKKGIVLINSVGVIDGDYYNNQVNEGHIFAQMQNITDQAVILEEGERIVQAVFAPFLLADDDQATGMRTGGFGSTGKMKKIRLSKFIKMIVVILFLISVAASFYFFHVAQVRDDKSFISNGQRKPGNSLYAYDKSFDKLLKQKIEMTNQNIKQVAWYVPAVKKTHKTAVVVHGFANSKENMKAYGWLFHKLGYNVLMPDNIAHGESHGQLIGYGWNDRENIIKWTEMIVDKNPSSQITLFGVSMGGATVMMASGEKLPSQVVNIIEDCGYSSVWDELKFQAKEMYGLPAFPLLYEVSTISKIRAGFSYGQASSVEQLKKNNLPALFIHGDKDNFVPTSMVYDNYKATAGKKELYIVKGAKHAKSFETEPEKYEKRISSFLKKYEKMTKYIFVTGGVVSSIGKGIVAASLGRLLKNRGLKVTIQKFDPYINIDPGTMSPYQHGEVYVTDDGAETDLDLGHYERFIDINLNKYSNVTTGKIYSEVLKKERRGEYLGATVQVIPHVTDALKEKIKRAATTTDSDVIITEVGGTVGDIESLPFLEALRQMKADVGSDNVMYIHTTLLPYLKAAGEMKTKPTQHSVKELRGLGIQPNMLVIRTEQPAGQSIKNKLAQFCDVAPEAVIESLDVDHIYQIPLNMQAQNMDQIVCDHLKLETPAADMTEWSAMVDKVMNLEKKVKIALVGKYVELPDAYLSVVEALKHSGYVNDVAIDLKWVNAAEVTEDNIKELVGDADGIIVPGGFGQRGSEGKIEAIRYARENDVPMLGVCLGMQLTCVEFARNVLNLHGANSAELDPKTPFPIIDIMRDQIDIEDMGGTLRLGLYPCKLKSGSRAAAAYNNQEVVQRRHRHRYEFNTKFREQFEAAGFVFSGVSPDNRLMEVVELPEKKFFVAAQYHPELQSRPNHAEELYTAFVTAAVENMKMELEVFAGQEKSELSMIEVARAILEQRGRDNEMYFSDLVNDIQTYLGKSDSAIRESLPFFYSDLNTDGSFIPLGENKWGLRSWYAIDEIDEEIITLEEDEDGAPKRKKKRVNAFMDGDEDAIDYNDDDPEDEDFTEETPSLEYDEENPDDEKSEVESYDSEINEIIPDEDLDEDVEINEEDDEEEEEEEEVMSTSFENKATNRGIITFTISQDEIKPALDQAFNKVKKDLNVPGFRKGHMPRTVFNQKFGEEALYENALNLVLPKAYEAAVAELGLDVVAQPKIDVVSMEKGQDWKLTAEVVTKPEVKLGDYKDLSVEVDASKEVSDEEVDAKVERERNNLAELTVKDGEAAQGDTVVIDFVGSVDGVEFDGGKGDNFSLELGSGQFIPGFEEQLVGSKAGQTVDVNVTFPEDYQAEDLAGKDAKFVTTIHEVKTKEVPALDDELAKDIDDEVETLDELKAKYRKELESAKEIAFDDAVEGAAIELAVANAEIVELPEEMVHDEVHRAMNEFMGNMQRQGISPEMYFQLTGTTEEDLHKQYQADADKRVKTNLVIEAIAAAEGFEATDEEIEKEITDLASEYNMEADQVRGLLSADMLKHDIAMKKAVDVITSSATVKMKKVLTFLLCSLYFVSIPAISTEEPLTLSQNRRYALTQTVVDKEMYFDAIPERPTTKIEISSFQDEALTITGETLVPNTLLSIVSLTINSNGIPVFTLSNGQFIKASREAIFNDLVSKQQSVSLDYWLKPSFVTYEAPYTNGVSEVKNNLKPYSRVHLVEQAETEHGIYYKTDSGFWISVEDLSVADNRMAKVQEVLLEKYNKDKYGIYIKQLNTQTVAGINIDRSMYSASIAKLATLYASQEQVKLGKLSLDSKFEYKDNVNQFPNSYDPSGSGKLEKKADHKLYTVKELLEATAKESDNVATNMLGYYVNNQYDSMFQTQVDTISGMHWDMKKRQISPQAAGKMMEAIYYQNGDIVNYLSKTDFDNTRIPKNIPVKVAHKIGDAYDYKHDAAIVYAEQPFIMIIFTDKSSYDDITKIADDVYQVLKMITLEKFIDHLNVEEVLFTFFTKLISILLLIIAFVIVRQVINYLFEKTVNRSLAFSRQKVARQKTLAKLSHNVLNYTLYFFLFYWILSILGVPISSLLAGAGIAGVAIGLGAQGFLSDVVNGFFILLENQFDVGDIINVGTVSGTVTNVGIRTTQIHDFDGTLHFIPNRNITIVSNKSRSNMRAQIDIPLFVHTNLDQISDIVTKINEEYVSKHPAIVGEPTVFGPTTNANGQFVYRINIFTQNGAQFDIYAEFYKLYQKAILEEGIDLPTYNFSNNHSRMILDYNKLKQETKAIVVDIIERSALKKGQIFVLGLSSSEVSGGLIGKNSSSEIGEIIVEVILKELHSRGIYLAVQGCEHVNRALVVEAELAERQQLEVVNVVPNLHAGGSGQVAAFKLMTSPVEVEEIVAHAGIDIGDTSIGMHIKRVQVPLIPISRELGGAHVTALASRPKLIGGARAGYTSDPIRKFMRKEKTSQLVQLAIVTAISIVLGMFISIPTPTGFLTLLDAGIFFAAFYFGKKEGAVVGALAGFLIDLLKGYPNWMFFSLLIHGTQGYLAGLPGRRRLLGLISATLVMVLGYAIASGLMYGWGAVLPDIPGNIMQNMVGMVVGFALNKSLERVKKMKTRNVLAISGNDIFSGGGLHADLATYVVNKLHGFVAVTCLTAMSDKGFEVIPIEASILKQQLESLKDVEFGSIKLGLLPNVETAQVVLEFVKSKQECPVVLDPVLVCKENHDLEVSQLREQLIAFFPYADVITPNLVEAQLLTGLSIENLDQMKIAAEKLYDMGAKHVVIKGGNRLNAEEATDLYYDGERFETYVFPVVDANNTGAGCTFASSIASQLAMGKNVEDAVKMSKGFVYQAIKASDKYGVVQHFMTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDVGVHAYGQVIHFDLPQARDVEKLRFGLDTQCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIGRPKNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQFEASKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGNGLYLKEIIYEDEECFSNFRKMVTKVEEIRSYLIASIQNGKLAPGDRLPSIRQLANQFSCNKDTVQRVLMELRFDNYIYAKPRSGYYVFDSHQEEVEEGVSLPNSEIANIAYDDFRLCLNETLIGREDYLFNYYYRQEGLLDLSKAVAKLMEETGVYVPLDDIVITAGTQQALFILTQVTFPNRKSRVLIEEPTYPRMIELIKTQNLPYETISRGTHGIDFQRLEEIFQTQSIKFFYVIPRMHNPLGTSYNPVEMKRLIEMAEKYDVYIVEDDYMSDFASQSPLHYYDTHGRVIYLKSFSKAIFPALRLAAICLPQALKSTFMAYKKLMDYDTNLILQKALALYIENGLYAKNSQYLKYRYQKDLANSKSILADHPNLPSYSLHHDSVLFDCSKLDNFKILRQYGDTLENYFCQKSHQSLLQVKNDSCLKQFLGSLMNNTEFYDRLGVSKDASQDEIKKAYRRMSKKYHPDINKETGAEEKYKEVQEAYETLSDTQKRAAYDQYGAAGANGGFGGFDGGGFGGFDGGGFGGFEDIFSSFFGGGGMRNPNAPRQGDDLQYRVNLSFEEAIFGAEKEVSYNRESSCHTCSGSGAKPGTSPVTCQKCHGSGVINVDTQTPLGTMRRQVTCDVCQGSGQEIKEKCPTCHGTGHEKKTHKVSVKIPAGVETGQQIRLTGQGEAGFNGGPYGDLFVIINVLPSQQFERNGSTIYYTLNISFVQAALGDTIDIPTVHGAVEMSIPAGTQTGKTFRLRGKGAPKLRGGGQGDQHVTVNIVTPTKLNDAQKEALHAFAEASGDKMVHPKKKGFFDKVKDALDVDMSKIIGIDLGTTNSAVAVLEGTESKIIANPEGNRTTPSVVSFKNGEIIVGDAAKRQAVTNPDTVISIKSKMGTSEKVSANGKEYTPQEISAMILQYLKGYAEDYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLEVERIVNEPTAAALAYGMDKTDKDEKILVFDLGGGTFDVSILELGDGVFDVLATAGDNKLGGDDFDQKIIDFLVEEFKKENGIDLSQDKMALQRLKDAAEKAKKDLSGVTQTQISLPFITAGSAGPLHLEMSLSRAKFDDLTRDLVERTKTPVRQALSDAGLSLSEIDEVILVGGSTRIPAVVEAVKAETGKEPNKSVNPDEVVAMGAAIQGGVITGDVKDVVLLDVTPLSLGIETMGGVFTKLIDRNTTIPTSKSQVFSTAADNQPAVDIHVLQGERPMAADNKTLGRFQLTDIPAAPRGIPQIEVTFDIDKNGIVSVKAKDLGTQKEQHIVIQSNSGLTDEEIDKMMKDAEANAEADAKRKEEVDLKNEVDQAIFATEKTIKETEGKGFDTERDAAQSALDELKKAQESGNLDDMKAKLEALNEKAQALAVKLYEQAAAAQQAAQGAEGAQSADSSSKGDDVVDGEFTEKMSEEIKKDDLQEEVEATETEETVEEVIEEIPEKSELELANERADEFENKYLRAHAEMQNIQRRSSEERQQLQRYRSQDLAKAILPSLDNLERALAVEGLTDDVKKGLEMTRDSLIQALKEEGVEEVEVDSFDHNFHMAVQTLPADDEHPADSIAEVFQKGYKLHERLLRPAMVVVYNMITQRQNDILNLIVELFTQTHEPVGSKALQRTIDSSSATIRNDMAKLEKLGLLEKAHTSSGRMPSPAGFKYFVEHSLRLDSIDEQDIYHVIKAFDFEAFKLEDMLQKASHILSEMTGYTSVILDVEPARQRLTGFDVVQLSNHDALAVMTLDESKPVTVQFAIPRNFLTRDLIAFKAIVEERLLDGSVMDIHYKLRTEIPQIVQKYFVTTDNVLQLFDYVFSELFLETVFVAGKVNSLTYSDLSTYQFLDNEQQVAISLRQSLKEGEMASVQVADSQEAALADVSVLTHKFLIPYRGFGLLSLIGPIDMDYRRSVSLVNIIGKVLAAKLGDYYRYLNSNHYEVHMSYSNLKLFALSSNKELAKKVSQTIGIPLGQSTVRQFSDGEIQVNIEESIRGHHVFILQSTSSPVNDNLMEILIMVDALKRASAESVSVVMPYYGYARQDRKARSREPITSKLVANMLEVAGVDRLLTVDLHAAQIQGFFDIPVDHLMGAPLIADYFDRQGLVGDDVVVVSPDHGGVTRARKLAQCLKTPIAIIDKRRSVTKMNTSEVMNIIGNIKGKKCILIDDMIDTAGTICHAADALAEAGATAVYASCTHPVLSGPALDNIQNSAIEKLIVLDTIYLPEERLIDKIEQISIAELIGEAIIRIHEKRPLSPLFEMNKLKMTKNLLLTGFLSFNDGKLDTNYFSCIIKYIISYQEVMMTLEKRFNKYLDRIEVSLIRQFDQSISDIPGMVKLTLGEPDFTTPDHVKEAAKSAIDANQSYYTGMSGLLALRQAAADFAKDKYNLTYNPDCEILVTIGATEALSASLIAILEAGDVVLLPAPAYPGYEPIVNLVGADIVEIDTRENDFRLTPEMLETAIIQQGEKLKAVLLNYPTNPTGITYSRQEIAALAEVLKKYDIFVISDEVYSELTYTGQQHVSIAEYLPNQTILINGLSKSHAMTGWRVGLVYAPEAFIAQIIKSHQYMVTAASTISQFAGVEALSVGKNDTLPMRQGYIKRRDYIIDKMSKLGFKIIKPSGAFYIFAKIPDSYPQDSFKFCQDFAYQQAVAIIPGVAFGKYGEGYIRLSYAASMEVIETAMARLKVFMESYEGMRVSQTYGLVLYNRNYREDDKLVKIFTETEGKRMFFVKHASKSKFNAVLQPLTIAHFILKINDNGLSYIDDYKEVLAFQETNSDLFKLSYASYITSLADVAISDNVADAQLFIFLKKTLELIEDGLDYEILTNIFEVQLLERFGVALNFHDCVFCHRVGLPFDFSHKYSGLLCPNHYYKDERRNHLDPNMLYLINRFQSIQFDDLQTISVKPEMKLKIRQFLDMIYDEYVGIHLKSKKFIDDLSSWGSIMKSDMNKWLVKASSLVVLGGMVLSAGSRVLADTYVRPIDNGRITTGFNGYPGHCGVDYAVPTGTIIRAVADGTVKFAGAGANFSWMTDLAGNCVMIQHADGMHSGYAHMSRVVARTGEKVKQGDIIGYVGATGMATGPHLHFEFLPANPNFQNGFHGRINPTSLIANVATFSGKTQASAPSIKPLQSAPVQNQSSKLKVYRVDELQKVNGVWLVKNNTLTPTGFDWNDNGIPASEIDEVDANGNLTADQVLQKGGYFIFNPKTLKTVEKPIQGTAGLTWAKTRFANGSSVWLRVDNSQELLYKMIETMSLDDMREYLGQDQIPEDFDDFWKKQTMKYQGNIEYRLDKKDFNITFAQAYDLHFKGSNNSIVYAKCLFPKTNKPYPVVFYFHGYQNQSPDWSDQLNYVAAGYGVVSMDVRGQAGQSQDKGHFDGITVKGQIVRGMISGPNHLFYKDIYLDVFQLIDIIATLESVDSNQLYSYGWSQGGALALIAAALNPKIVKTVAVYPFLSDFRRVLDLGGVSEPYDELFRYFKYSDPFHKTENNVLKTLAYIDVKNFAHRISCPVVLLTALKDDICPPSTQFAIFNRLTSTKKHLLLPDYGHDPMTVQVKDHIFDQLTGSQFTKQKIEMTRTVAIDIGGTMIKHGIVDNLGCIVEASELATEAYKGGPGILQKVCQIIDNYLAEGSIDGIAISSAGMVDPDEGCIFYSGPQIPNYAGTQFKKVLEDTYQVRTEIENDVNCAGLAEAVSGSAKDSSIALCLTIGTGIGGCLIIDKTVFHGFSNSACEVGYMHLSDGDFQDLASTTALIADVAKAHGDEISRWDGRRIFQEAKKGNEKCIASIDRMINYLGQGIANMVYVVNPEKVVLGGGIMAQKDYLQDKLSESLKRNLVTSLAEKTAIVFAQHENQAGMLGAYYHFKNRGMKDLQKYQGIIPAFYACYDDKGDICPERVKALTNYFIDKGVQGLYVNGSSGECIYQSVADRKLVLENVMSVAKGKLTVIAHVACNNTKDSVELAMHAEAIGVDAIAAIPPIYFRLPEYAIADYWNTISQAAPQTDFIIYNIPQLAGVALTSDLYRKMLQNPQVIGVKNSSMPVQDIQNFVAIGGENHIVFNGPDEQFLGGRLMGAAAGIGGTYGVMPELYLTLNQLIVDKDLEKARELQFTINDIITKLCSGHGNMYAVIKAVLEINEQLTIGSVRLPLASVTEEDKPIIKEAAEMIRHAKKQFCMKKANQLIAAIFDVNNPFMQGCNVVFDLALLNLLFMITCLPLVTIGAAKISLYRTLWQKLEGDQTNLLILYIKHLKKEWFQGMLLGLVELSILVVIIFDLTILHYQIGFIVSFLKITCYAFLLLTVMTSIYLFPMAARYEMSLLDTVKKSFIMACLNLKWTGVLMFLLIMTWFIMVQSSLLFMLTVSAIFIFAYTAFAYFKIIILQKQFAYFSKQQGDYQMIYDHLLNLTHYKDINPNLDLAIDYLLSHDLRNLDIGTYHISPEVILMVQSNQLSESFDHIFEYHKKYLDIHYVIEGHEVIKLGKGDKVEVEEYLGDIGFIKCSEETSFDLRDNYIAFFFPEEAHQPNGMGSLGNYVKKGVLKVLMAMKKKTFSAYNFLTALILCLLTVLFIFPFYWIMTGAFKSQPDTIIIPPQWWPKAPTLENFKALTVQNPALRWLWNSVFISIMTMFLVCCTSSMAGYVLAKKRFYGQKILFSLFIAAMALPKQVVLVPLVRIINFMGIHDTLWAVILPLVGWPFGVFLMKQFSENIPTELLESAKIDGCGEIRTFINVAFPIVKPGFAALAIFTFINTWNDYFMQLVMLTSRNNLTISLGVATMQAEMATNYGLIMAGAALAAVPIVTVFLVFQKSFTQGITMGAVKGMRTNKLKMRETMIAYAFLAPILLFFLIFVFAPMVMGFVTSFFNYSMTQFTFIGLANYNRMFHDSIFMKSLINTVIIVIGSVPVVVFFSLFVAANTYEKNVFSRSFYRCVFFLPVVTGSVAVTVVWKWIYDPMSGILNYILKSGHVIEQNISWLGDKHWALLAIIIILLTTSVGQPIILYIAAMGNIDNSLCEAARVDGANEMQVFWQIKWPSLLPTTLYIAVITTINSFQCFALIQLLTSGGPNYSTSTLMYYLYEKAFKLSEYGYANTMGVFLAVMIALISFAQFKILGNDVEYMSIKKSVIGFCLGAAALSMFACVDSSQSVMAAEKDKVEITWWAFPTFTQEKAKDGVGTYEKKVIKAFEKKNPNIKVKLETIDFTSGPEKITTAIEAGTAPDVLFDAPGRIIQYGKNGKLADLNDLFTDQFIKDVNNKNIIQASKSGDKAYMYPISSAPFYMAFNKKMLKDAGVLKLVKEGWTTSDFEKVLKALKNKGYTPGSFFANGQGGDQGPRAFFANLYSAPITDKEVTKYTTDTKNSVKSMKKIVEWIKKGYLMNGSQYDGSADIQNFANGQTAFTILWAPAQPKTQAKLLESSKVDYLEVPFPSEDGKPDLEYLVNGFAVFNNKDENKVKASKKFITFIADDKKWGPKDVIRTGAFPVRTSFGDLYKGDKRMMKISKWTQYYSPYYNTIDGFSEMRTLWFPMVQSVSNGDEKPADALKDFTQKANDTIKKAAKMPHLSKEAFKKQIKNGIIVSCQALPGEPLYTESGGVMPLLALAAQEAGAVGIRANSVRDIKEIQEVTNLPIIGIIKREYPPQEPFITATMTEVDQLASLDIAVIALDCTLRERHDGLSVVEFIQKIKRKYPEQLLMADISTFEEGKNAFEAGVDFVGTTLSGYTDYSRQEEGPDIELLNKLCQAGIDVIAEGKIHTPKQANEINHIGVAGIVVGGAITRPKEIAERFISGLSMKMNKKVLLTSTMAASLLSVASVQAQETDTTWTARTVSEVKADLVKQDNKSSYTVKYGDTLSVISEAMSIDMNVLAKINNIADINLIYPETTLTVTYDQKSHTATSMKIETPATNAAGQTTATVDLKTNQVSVADQKVSLNTISEGMTPEAATTIVSPMKTYSSAPALKSKEVLAQEQAVSQAAANEQVSPAPVKSITSEVPAAKEEVKPTQTSVSQSTTVSPASVAAETPAPVAKVAPVRTVAAPRVASVKVVTPKVETGASPEHVSAPAVPVTTTSPATDSKLQATEVKSVPVAQKAPTATPVAQPASTTNAVAAHPENAGLQPHVAAYKEKVASTYGVNEFSTYRAGDPGDHGKGLAVDFIVGTNQALGNKVAQYSTQNMAANNISYVIWQQKFYSNTNSIYGPANTWNAMPDRGGVTANHYDHVHVSFNKMTKRALISVSDKSGIIDFAKELKNLGWDIISTGGTKVALDDAGVETIAIDDVTGFPEMMDGRVKTLHPNIHGGLLARRDADSHLQAAKDNNIELIDLVVVNLYPFKETILRPDVTYDLAVENIDIGGPSMLRSAAKNHASVTVVVDSADYATVLGELADASQTTFKTRQRLAAKAFRHTAAYDALIAEYFTAQVGEAKPEKLTITYDLKQAMRYGENPQQDADFYQKALPTDYSIASAKQLNGKELSFNNIRDADAAIRIIRDFKDSPTVVALKHMNPCGIGQADDIETAWDYAYEADPVSIFGGIVVLNREVDAATAEKMHPIFLEIIIAPSYSEEALAILTNKKKNLRILELPFDAQAASEVEAEYTGVVGGLLVQNQDVVAENPSDWQVVTDRQPTEQEATALEFAWKAIKYVKSNGIIITNDHMTLGLGAGQTNRVGSVKIAIEQAKDHLDGAVLASDAFFPFADNIEEIAAAGIKAIIQPGGSVRDQESIDAANKHGLTMIFTGVRHFRHMELIFRIFEMKKTLYITNKLFFANWFVPVIGAVLIQVIGIIVSRRLVVKLLPDDYKFNLYIALLLFVPILASILLFLIYFQKRDFTSLGFTKDNNVLTTISGFITGSLLMFFIYICHWLSGFVEISSSNSFSFGPFFFLFLAYFIQSLTEEILFRGYVMTTVTKFKGSFAGVLCNSMLFSFIHFRNYGITAIALFNLFLLGIIFSILFNMTKNILFVTGVHTTWNFTMGCVLGNKVSGGDSPVSLFRITENSSFALWNGGDFGFEGGVLCSLILVGCLAYFSLESVRVSVRYMKLVKNLEIVESIFGDWDETIIWSCVQGIMGEVFVDSLDQPKSSLAKLGRKSSFGFLAGQPTLFLLEVCSGEDIILVPQHKGWSDLIESTYGQNAHSFKRYATKKDTLFERSRLEKFVTQLPNGFELRAIDEKVYNSCLEKEWSQDLVANYATYQYYKKQGIGYVVYYQGNIIAGASSYSTYKNGIEIEVDTHPDFRRRGLATIVAAQLILTCLDKGIYPSWDAHTRTSLNLSEKLGYEFSHEYIAYEIDMKIAVFASGNGSNFQVIAEQFQVSFVFSDHRDAYVLERAQNLAIPSFAFELKEFENKAAYEQAVVDLLDKHEIDLVCLAGYMKIVGETLLSAYEGRIINIHPTYLPEFPGAHGIKDAWEAGVDQSGVTIHWVDSGVDTGQVIQQVHVPRLADDSLESFETRIHETEYQLYPAVLDSLGIKRKMMSNMTLYIIANPHAGNKNASTIVGKIQELYHTEDISVFYTEQKDDEKKQVINILRSFKESDHLMIIGGDGTLSKVMTYLPQHIPCTYYPVGSGNDFARALKIPNLKETLTAIQTERLKEINCFIYDKGLILNSLDLGFAAYVVWKASNSKIKNILNRYRLGKITYIVIAIKSLLHSSKVQVLVEGETGQQIKLNDLYFFALANNTYFGGGITIWPKASALTAELDMVYAKGHTFLKRLSILLSLVFKRHTTSKSIKHQTFKAMTVYFPKNSLIEIDGEIVELDQISLKCQKRYLYMMSEKNAYAQSGVDVEAGYEVVERIKKHVARTERAGVMGALGGFGGMFDLSQTGVKEPVLISGTDGVGTKLMLAIKYDKHDTIGQDCVAMCVNDIIAAGAEPLYFLDYVATGKNEPAKLEQVVAGVAEGCVQASAALIGGETAEMPGMYGEDDYDLAGFAVGVAEKSQIIDGSKVKEGDILLGLASSGIHSNGYSLVRRVFADYTGDEVLPELEGKQLKDVLLEPTRIYVKAALPLIKEELVNGIAHITGGGFIENVPRMFADDLAAEIDEDKVPVLPIFKALEKYGDIKHEEMFEIFNMGVGLMLDVNPENVDRVKELLDEPVYEIGRIIKKADDSVVIKMTYEVKSLNEECGVFGIWGYPQAAQVTYFGLHSLQHRGQEGAGIISNDNGKLYGYRNVGLLSEVFKNQSELDNLTGNAAIGHVRYATAGSADIRNIQPFLYKFHDGQFALCHNGNLTNAISSRKELEKQGAIFNASSDTEILMHLIRRSHNPSFMGKVKEALSTVKGGFAYLLMTEDKLIAALDPNAFRPLSIGQMQNGAWVISSETCAFEVVGAKWVRDVEPGEVILIDDSGIQCDRYTDETQLAICSMEYVYFARPDSTIHGVNVHTARKNMGKRLAQEFKQDADIVIGVPNSSLSAAMGFAEESGLPNEMGLVKNQYTQRTFIQPTQELREQGVRMKLSAVSGVVKGKRVVMIDDSIVRGTTSRRIVGLLREAGATEVHVAIASPELKYPCFYGIDIQTRRELISANHAVDEVCDIIGADSLTYLSIDGLIKSIGLETKAPNGGLCVAYFDGHYPTPLYDYEEEYLRSLEEKTSFYIQKVKMNKRIFVEKKADFGIKSASLVKELTHNLQLASLKDLRIVQVYDVFNLAEDLLARAEKHIFSEQVTDRLLTEAEITAELDKVAFFAIEALPGQFDQRAASSQEALLLLGSDSQVKVNTAQLYLVNKDIAEAELEAVKNYLLNPVDSRFKDITLPLEVQAFSVSDKTISNLDFFETYQADDFAAYKAEQGLAMEVDDLLFIQDYFKSIGRVPTETELKVLDTYWSDHCRHTTFETELKNIDFSASKFQKQLQATYDKYIAMRDELGRSEKPQTLMDMATIFGRYERANGRLDDMEVSDEINACSVEIEVDVDGVKEPWLLMFKNETHNHPTEIEPFGGAATCIGGAIRDPLSGRSYVYQAMRISGAGDITTPIAETRAGKLPQQVISKTAAHGYSSYGNQIGLATTYVREYFHPGFVAKRMELGAVVGAAPKENVVREKPEAGDVVVLLGGKTGRDGVGGATGSSKVQTVESVETAGAEVQKGNAIEERKIQRLFRDGNVTRLIKKSNDFGAGGVCVAIGELADGLEIDLDKVPLKYQGLNGTEIAISESQERMSVVVGPSDVDAFIAACNKENIDAVVVATVTEKPNLVMTWNGETIVDLERCFLDTNGVRVVVDAKVVDKDLTVPEARTTSAETLEADMLKVLSDLNHASQKGLQTIFDSSVGRSTVNHPIGGRYQITPTESSVQKLPVQYGVTTTASVMAQGYNPYIAEWSPYHGAAYAVIEATARLVATGADWSRARFSYQEYFERMDKQAERFGQPVSALLGSIEAQIQFGLPSIGGKDSMSGTFEELTVPPTLVAFGVTTADSRKVLSPEFKAAGENIYYIPGQAISEDIDFDLIKANFSQFEAIQAQHKITAASAVKYGGVLESLALMTFGNRIGASVEIAELDSSLTAQLGGFVFTSVEEIADVVKIGQTQADFTVTVNGNDLAGASLLSAFEGKLEEVYPTEFEQVDAIEEVPAVVSDVVIKAKEIIEKPVVYIPVFPGTNSEYDSAKAFEQVGASVNLVPFVTLNEAAIAESVDTMVANIAKANIIFFAGGFSAADEPDGSAKFIVNILLNEKVRAAIDSFIEKGGLIIGICNGFQALVKSGLLPYGNFEEAGETSPTLFYNDANQHVAKMVETRIANTNSPWLAGVEVGDIHVIPVSHGEGKFVVSASEFAELRDNGQIWSQYVDFDGQPSMDSKYNPNGSVNAIEGITSKNGQIIGKMGHSERWEDGLFQNIPGNKDQKLFESAVKYFTGKMTNQLIYTGKAKDIYSTKDENVIRTVYKDQATMLNGARKETIDGKGALNNQISSLIFEKLNMAGVVTHYIEQISKNEQLNKKVDIIPLEVVLRNVTAGSFSKRFGVEEGHVLETPIVEFYYKNDNLNDPFINDEHVKFLGIVNDEEIAYLKGETRHINELLKDWFAQIGLNLIDFKLEFGFDKDGKIILADEFSPDNCRLWDADGNHMDKDVFRRDLGSLTDVYQVVLEKLIALMSRDEVFEKMLELLRQQLGDPQLDITPESSLHDDLAIDSIALTEFIINLEDVFHLEIPDEAVEHMSSVQQLLDYIIEHKMKKIAIDAMGGDYAPKAIVEGVNQAISDFSDIEVQLYGDQKKIEKYLTVTERVSIIHTEEKINSDDEPAKAVRRKKQSSMVLGAKAVKDGVAQAFISAGNTGALLAAGLFVVGRIKGVDRPGLMSTMPTLDGVGFDMLDLGANAENTASHLHQYAILGSFYAKNVRGIEVPRVGLLNNGTEETKGDSLHKEAYELLAAEPSINFIGNIEARDLMSSVADVVVTDGFTGNAVLKTMEGTAMSIMGSLKSSIKSGGVKAKLGALLLKDSLYQLKDSMDYSSAGGAVLFGLKAPIVKCHGSSDSKAVYSTLKQVRTMLETQVVDQLVDAFTDEMRKRFSLLNFIVVTFIFFFFILFPLLNHKGKVDANSRQSVTYTKEEFIQKIVPDAQDLGKSYGIRPSFIIAQAALDSDFGEKILANKYHNLFGLLAEPGTPSITLNDSSTGKKQEKQFTHYKSWKYSMYDYLAHIKSGATGKKDSYTIMVSVKNPKTLVQKLQDSGFDNDKKYAKKMTEIIDLYDLTRYDK

From 2a8c54cba64002fa482793f8d395b8c61b38bf79 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 18:45:48 +0200
Subject: [PATCH 92/97] update test check in NSSTAT

---
 tools/chewbbaca/NSStats.xml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index e4301fdb4a0..ea3608bb0d1 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -30,11 +30,12 @@
         <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name}"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_exit_code="0">
             <param name="mode" value="species" />
-            <output name="NSStats" file="NSStats.txt" compare="diff">
+            <output name="NSStats" file="NSStats.txt">
                 <assert_contents>
                     <has_text_matching expression="Streptococcus pyogenes"/>
+                    <has_text_matching expression="Salmonella enterica"/>
                     <has_text_matching expression="Clostridium neonatale"/>
                 </assert_contents>
             </output>

From 969e98b88e923b7458e683e60ea9b6aadac05d64 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Thu, 11 Apr 2024 19:02:29 +0200
Subject: [PATCH 93/97] update test data

---
 tools/chewbbaca/test-data/NSStats.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/chewbbaca/test-data/NSStats.txt b/tools/chewbbaca/test-data/NSStats.txt
index 6b96ee40a50..cdac0e67d25 100644
--- a/tools/chewbbaca/test-data/NSStats.txt
+++ b/tools/chewbbaca/test-data/NSStats.txt
@@ -8,7 +8,7 @@ Contacts: imm-bioinfo@medicina.ulisboa.pt
 =======================
   chewBBACA - NSStats
 =======================
-Started at: 2024-04-03T10:24:19
+Started at: 2024-04-11T17:01:56
 
 
 Retrieving data...
@@ -35,5 +35,5 @@ Clostridium neonatale               16          1          2350       13115
 ------------------------------------------------------------------------------
 
 
-Finished at: 2024-04-03T10:24:23
+Finished at: 2024-04-11T17:02:00
 Took  0m 4s.

From bfd3a5dae3f7ca3f919a0911315cb340f6b37f5f Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 12 Apr 2024 11:11:20 +0200
Subject: [PATCH 94/97] updated test for NSSTATS. line_diff

---
 tools/chewbbaca/NSStats.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index ea3608bb0d1..8d3fc06b83d 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -32,7 +32,7 @@
     <tests>
         <test expect_exit_code="0">
             <param name="mode" value="species" />
-            <output name="NSStats" file="NSStats.txt">
+            <output name="NSStats" file="NSStats.txt" lines_diff="3">
                 <assert_contents>
                     <has_text_matching expression="Streptococcus pyogenes"/>
                     <has_text_matching expression="Salmonella enterica"/>

From dcda29ded7440433e68807509773ceefedcbe88e Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 12 Apr 2024 12:23:05 +0200
Subject: [PATCH 95/97] Update line_diff

---
 tools/chewbbaca/NSStats.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index 8d3fc06b83d..87332f3a8d2 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -32,7 +32,7 @@
     <tests>
         <test expect_exit_code="0">
             <param name="mode" value="species" />
-            <output name="NSStats" file="NSStats.txt" lines_diff="3">
+            <output name="NSStats" file="NSStats.txt" compare="diff" lines_diff="4">
                 <assert_contents>
                     <has_text_matching expression="Streptococcus pyogenes"/>
                     <has_text_matching expression="Salmonella enterica"/>

From e306bfb187da698d09f91aaa4ed780bcaac12dd6 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 12 Apr 2024 13:48:36 +0200
Subject: [PATCH 96/97] update line_diff

---
 tools/chewbbaca/NSStats.xml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index 87332f3a8d2..0ad96ca1885 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -32,11 +32,10 @@
     <tests>
         <test expect_exit_code="0">
             <param name="mode" value="species" />
-            <output name="NSStats" file="NSStats.txt" compare="diff" lines_diff="4">
+            <output name="NSStats" file="NSStats.txt" compare="diff" lines_diff="5">
                 <assert_contents>
-                    <has_text_matching expression="Streptococcus pyogenes"/>
-                    <has_text_matching expression="Salmonella enterica"/>
-                    <has_text_matching expression="Clostridium neonatale"/>
+                    <has_text_matching expression="Streptococcus pyogenes\s+1\s+1\s+3044\s+398511"/>
+                    <has_text_matching expression="Clostridium neonatale\s+16\s+1\s+2350\s+13115"/>
                 </assert_contents>
             </output>
         </test>

From 47ed2acb725155e2bc02aa03979769217bb152e4 Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Fri, 12 Apr 2024 14:12:16 +0200
Subject: [PATCH 97/97] update on NSSTATS test

---
 tools/chewbbaca/NSStats.xml           |  2 +-
 tools/chewbbaca/test-data/NSStats.txt | 39 ---------------------------
 2 files changed, 1 insertion(+), 40 deletions(-)
 delete mode 100644 tools/chewbbaca/test-data/NSStats.txt

diff --git a/tools/chewbbaca/NSStats.xml b/tools/chewbbaca/NSStats.xml
index 0ad96ca1885..3794f4e5fb2 100644
--- a/tools/chewbbaca/NSStats.xml
+++ b/tools/chewbbaca/NSStats.xml
@@ -32,7 +32,7 @@
     <tests>
         <test expect_exit_code="0">
             <param name="mode" value="species" />
-            <output name="NSStats" file="NSStats.txt" compare="diff" lines_diff="5">
+            <output name="NSStats">
                 <assert_contents>
                     <has_text_matching expression="Streptococcus pyogenes\s+1\s+1\s+3044\s+398511"/>
                     <has_text_matching expression="Clostridium neonatale\s+16\s+1\s+2350\s+13115"/>
diff --git a/tools/chewbbaca/test-data/NSStats.txt b/tools/chewbbaca/test-data/NSStats.txt
deleted file mode 100644
index cdac0e67d25..00000000000
--- a/tools/chewbbaca/test-data/NSStats.txt
+++ /dev/null
@@ -1,39 +0,0 @@
-
-chewBBACA version: 3.3.3
-Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
-Github: https://github.com/B-UMMI/chewBBACA
-Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
-Contacts: imm-bioinfo@medicina.ulisboa.pt
-
-=======================
-  chewBBACA - NSStats
-=======================
-Started at: 2024-04-11T17:01:56
-
-
-Retrieving data...
-
-------------------------------------------------------------------------------
-Species                             id       #schemas     #loci      #alleles 
-------------------------------------------------------------------------------
-Streptococcus pyogenes              1           1          3044       398511  
-Acinetobacter baumannii             2           1          2390       701606  
-Arcobacter butzleri                 3           1          7474       82419   
-Campylobacter jejuni                4           1          2794       299214  
-Escherichia coli                    5           1          7601      2963736  
-Listeria monocytogenes              6           1          1748       371020  
-Yersinia enterocolitica             7           1          6344       154555  
-Salmonella enterica                 8           1          8558      2879459  
-Streptococcus agalactiae            9           1          3641       248987  
-Brucella melitensis                 10          1          2762       11222   
-Brucella                            11          1          1764       78557   
-Clostridium perfringens             12          1          1431       152324  
-Clostridium chauvoei                13          1          2223        7711   
-Bacillus anthracis                  14          1          3803       52474   
-Klebsiella oxytoca                  15          1          4201       132939  
-Clostridium neonatale               16          1          2350       13115   
-------------------------------------------------------------------------------
-
-
-Finished at: 2024-04-11T17:02:00
-Took  0m 4s.