--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ExtractCgMLST.xml	Wed Sep 25 14:12:35 2024 +0000
@@ -0,0 +1,62 @@
+<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>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py ExtractCgMLST
+        --t $threshold
+        #if $genes2remove:
+            --r '$genes2remove'
+        #end if 
+        #if $genomes2remove:
+            --g '$genomes2remove'
+        #end if 
+        -i '$input_file' -o 'output'
+    ]]></command>
+    <inputs>
+        <param argument="--input-file" type="data" label="Allelic Profiles" format="tabular"/>
+        <section name="advanced" title="Advanced options">
+            <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/>
+            <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values as a space-separated list.">
+                <validator type="regex">[ .0-9]+</validator>
+            </param>
+            <param argument="--genes2remove" type="data" format="tabular" label="List of genes  to exclude from analysis" optional="true" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process."/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="output_collection" type="list" format="html,tsv,txt" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="__name_and_ext__" directory="output"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="results_alleles.tsv"/>
+            <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>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
+
+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. 
+
+.. class:: infomark
+
+**Note**
+
+The user can define a **space-separated** list of values for --threshold
+    </help>
+    <expand macro="citations" />
+</tool>
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