Mercurial > repos > genouest > peptimapper_clustqualify

annotate clust_qualify.xml @ 0:1a673951d076 draft

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"planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
author genouest
date Fri, 10 Dec 2021 10:36:29 +0000
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children d913a2af45dc
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1 <tool id="peptimapper_clustqualify" name="ClustQualify" version="2.0">
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2 <description>annotates clusters according to gff annotation files</description>
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3 <requirements>
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4 <container type="docker">dockerprotim/peptimapper</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 mkdir 'repo' &&
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8 unzip '${gffdir}' -d repo &&
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9 LXQualify '$clustersfile' repo &&
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10 mv '${clustersfile}.txt' '$clustersQualifResults'
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11 ]]></command>
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12 <inputs>
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13 <param name="clustersfile" type="data" format="txt" label="Clusters file" help="Clusters file generated by PepMatch" />
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14 <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"/>
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15 </inputs>
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16 <outputs>
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17 <data format="txt" name="clustersQualifResults" label="${clustersfile.element_identifier}.qual"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="clustersfile" value="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.txt"/>
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22 <param name="gffdir" value="clustqualify/gff3_files_repository.zip"/>
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23 <output name="clustersQualifResults" file="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.qual.txt"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27
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28 **Description**
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29
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30 ClustQualify : run LXQualify from the "peptimapper" docker.
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31 ClustQualify annotes clusters, generated from PepMatch, according to gff annotation files.
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32
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33 **Integrated by**
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34
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35 Laetitia Guillot Cloarec
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36 PROTIM Biogenouest proteomics Core Facility, Rennes
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37 May,2016
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38
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39 ]]></help>
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40 <citations>
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41 <citation type="bibtex">
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42 @misc{renameTODO,
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43 author = {Protim Core facility},
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44 year = {2016},
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45 title = {ClustQualify},
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46 url = {protim.eu},
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47 }
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48 </citation>
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49 </citations>
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50 </tool>