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| 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 |
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| <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} && | ||
|
There was a problem hiding this comment. please single-quote all file-path |
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| #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 | ||
| ]]></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" /> | ||
|
There was a problem hiding this comment. Please add help text from the documentation something like "Default is to get training file from the schema"
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| <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> | ||
|
There was a problem hiding this comment. optional, please do not set any value |
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| <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"/> | ||
|
There was a problem hiding this comment. This is also an optional one. Can you also please double check if it is an integer type? There was a problem hiding this comment. Yes it is an integer. |
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| <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/> | ||
|
There was a problem hiding this comment. This is an optional param. Please do not set any default values to optional params rather use |
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| <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> | ||
| <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> | ||
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| </inputs> | ||
| <outputs> | ||
| <collection name="allelecall_results" type="list" label="${tool.name} on ${on_string}: AlleleCall Results"> | ||
| <discover_datasets pattern="(?P<name>.+)\.tsv$" format="tabular" directory="./output"/> | ||
| </collection> | ||
| <collection name="allelcall_log" type="list" label="${tool.name} on ${on_string}: AlleleCall Logs"> | ||
| <discover_datasets pattern="(?P<name>.+)\.txt$" 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" 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"/> | ||
| </assert_contents> | ||
| </element> | ||
| <element name="results_alleles" ftype="tabular"> | ||
| <assert_contents> | ||
| <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> | ||
| <help><![CDATA[ | ||
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| 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: [email protected] | ||
|
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| ========================== | ||
| 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. | ||
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| -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) | ||
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| -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) | ||
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| -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) | ||
|
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| --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) | ||
|
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| --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) | ||
|
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| --l, --minimum-length MINIMUM_LENGTH Minimum sequence length accepted for a coding | ||
| sequence to be included in the schema. (default: | ||
| None) | ||
|
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| --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) | ||
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| --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) | ||
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| --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) | ||
|
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| --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) | ||
|
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| --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) | ||
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| 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 | ||
|
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||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> | ||
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| @@ -0,0 +1,119 @@ | ||||||
| <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> | ||||||
| </macros> | ||||||
| <expand macro="requirements" /> | ||||||
| <command detect_errors="exit_code"><![CDATA[ | ||||||
| mkdir ./input && | ||||||
| #for $file in $input_file | ||||||
| cp $file ./input/${file.element_identifier} && | ||||||
|
There was a problem hiding this comment. is
Suggested change
working instead of copying? |
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| #end for | ||||||
| chewBBACA.py CreateSchema | ||||||
| #if str($training_file) != 'None' | ||||||
| --ptf '$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="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> | ||||||
| <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> | ||||||
|
There was a problem hiding this comment. please check if There was a problem hiding this comment. The authors suggest to use prodigal file (training file) instead of the cds file. if the user uses the There was a problem hiding this comment. Yes, please. As a conditional and a test. |
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| </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" compare="sim_size"/> | ||||||
| </test> | ||||||
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| </tests> | ||||||
| <help><![CDATA[ | ||||||
| chewBBACA version: 3.3.3 | ||||||
|
There was a problem hiding this comment. Please create a useful help section, the parameters are already explained in the form, here you can describe the tool, the functionality and maybe where you can get the zip file from. |
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| 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: [email protected] | ||||||
|
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| ============================ | ||||||
| chewBBACA - CreateSchema | ||||||
| ============================ | ||||||
| usage: | ||||||
| Create schema from genome assemblies. | ||||||
|
|
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| positional arguments: | ||||||
| CreateSchema | ||||||
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| options: | ||||||
|
|
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| -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) | ||||||
|
|
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| -o, --output-directory OUTPUT_DIRECTORY Output directory where the process will store | ||||||
| intermediate files and create the schema's | ||||||
| directory. (default: None) | ||||||
|
|
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| --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) | ||||||
|
|
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| --t, --translation-table TRANSLATION_TABLE Genetic code used to predict genes and to translate | ||||||
| coding sequences. (default: 11) | ||||||
|
|
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| --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) | ||||||
|
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| 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> | ||||||
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please change for tools too