--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clust_qualify.xml	Fri Dec 10 10:36:29 2021 +0000
@@ -0,0 +1,50 @@
+<tool id="peptimapper_clustqualify" name="ClustQualify" version="2.0">
+    <description>annotates clusters according to gff annotation files</description>
+    <requirements>
+        <container type="docker">dockerprotim/peptimapper</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+mkdir 'repo' &&
+unzip '${gffdir}' -d repo &&
+LXQualify '$clustersfile' repo &&
+mv '${clustersfile}.txt' '$clustersQualifResults'
+    ]]></command>
+    <inputs>
+      <param name="clustersfile" type="data" format="txt" label="Clusters file" help="Clusters file generated by PepMatch" />
+      <param name="gffdir" type="data" format="data" label="GFF files repository" help="zipped repository : for upload a zip repository into Galaxy, install before and use 'no_unzip.zip' datatype and select it into your upload form otherwise Galaxy decompress uploaded zip datatype file automatically"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="clustersQualifResults" label="${clustersfile.element_identifier}.qual"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="clustersfile" value="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.txt"/>
+            <param name="gffdir" value="clustqualify/gff3_files_repository.zip"/>
+            <output name="clustersQualifResults" file="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.qual.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    **Description**
+
+    ClustQualify : run LXQualify from the "peptimapper" docker.
+    ClustQualify annotes clusters, generated from PepMatch, according to gff annotation files.
+
+    **Integrated by**
+
+    Laetitia Guillot Cloarec
+    PROTIM Biogenouest proteomics Core Facility, Rennes
+    May,2016
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+        @misc{renameTODO,
+        author = {Protim Core facility},
+        year = {2016},
+        title = {ClustQualify},
+        url = {protim.eu},
+        }
+        </citation>
+    </citations>
+</tool>