add ExtractCgMLST.xml

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: [email protected]
+
+=============================
+  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>