diff clust_to_gff.xml @ 0:691d8f3aeb1a draft

"planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"

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+++ b/clust_to_gff.xml	Fri Dec 10 10:34:56 2021 +0000
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+<tool id="peptimapper_clust_to_gff" name="ClustToGFF" version="2.0">
+    <description>add clusters locations into GFF files to be integrated into a genome viewer</description>
+    <requirements>
+        <container type="docker">dockerprotim/peptimapper</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+unzip '${gffdir}' -d gff &&
+mkdir "outputdir" &&
+LXClust2Gff gff/* outputdir '${clustersfile}' &&
+mv *.gff outputdir/ &&
+zip -r outputdir2 outputdir/* &&
+mv outputdir2.zip '${gfffiles}'
+    ]]></command>
+    <inputs>
+        <param name="clustersfile" type="data" format="txt" label="Clusters file" help="Clusters file generated by PepMatch" />
+        <param name="gffdir" type="data" label="GFF files repository" help="Zipped repository containing all organism GFF files" />
+    </inputs>
+    <outputs>
+        <data name="gfffiles" format="zip" label="GFF files including clusters locations" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="clustersfile" value="clusttogff/Gamete.5.3.2.5000.clust"/>
+            <param name="gffdir" value="clusttogff/gff3_files_repository.zip"/>
+            <output name="output" file="clusttogff/out.zip" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**Description**
+
+ClustToGFF : run LXClust2Gff from the "peptimapper" docker.
+ClustToGFF adds clusters locations, generated by PepMatch, into GFF annotation files to be integrated into a genome viewer.
+
+**Integrated by**
+
+Laetitia Guillot Cloarec
+PROTIM Biogenouest proteomics Core Facility, Rennes
+July,2017
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{renameTODO,
+            author = {Protim Core facility},
+            year = {2017},
+            title = {ClustToGFF},
+            url = {protim.eu},
+            }
+        </citation>
+    </citations>
+</tool>