--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/JoinProfiles.xml	Wed Sep 25 14:12:43 2024 +0000
@@ -0,0 +1,38 @@
+<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>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py JoinProfiles
+            -p ${str($input1).replace(',', ' ')}
+            -o 'JoinedProfile.tsv'
+            $common
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="tsv" multiple="true" label="AlleleCall results" />
+        <param argument="--common" type="boolean" truevalue="--common" falsevalue="" checked="false" label="Common" optional="true" help="Create file with profiles for the set of common loci" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="results_alleles.tsv,results_alleles2.tsv"/>
+            <output name="JoinedProfile" file="JoinedProfile.tsv" compare="diff"/>
+        </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 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>
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