Mercurial > repos > genouest > peptimapper_clustqualify

annotate clust_qualify.xml @ 1:d913a2af45dc draft

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"planemo upload commit bbcbc29ef60120ea945879874ca92fb098dda8bf"
author genouest
date Mon, 13 Dec 2021 14:13:08 +0000
parents 1a673951d076
children 52f3ceda99a4
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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 ln -s '$clustersfile' 'in.clusters' &&
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8 mkdir 'repo' &&
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9 unzip '${gffdir}' -d repo &&
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10 LXQualify 'in.clusters' repo &&
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11 mv 'in.clusters.txt' '$clustersQualifResults'
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12 ]]></command>
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13 <inputs>
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14 <param name="clustersfile" type="data" format="txt" label="Clusters file" help="Clusters file generated by PepMatch" />
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15 <param name="gffdir" type="data" format="data" label="GFF files repository" help="zipped repository : for upload a zip repository into Galaxy, install before and use 'no_unzip.zip' datatype and select it into your upload form otherwise Galaxy decompress uploaded zip datatype file automatically"/>
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="clustersQualifResults" label="${clustersfile.element_identifier}.qual"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <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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23 <param name="gffdir" value="clustqualify/gff3_files_repository.zip"/>
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24 <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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25 </test>
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26 </tests>
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27 <help><![CDATA[
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28
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29 **Description**
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30
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31 ClustQualify : run LXQualify from the "peptimapper" docker.
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32 ClustQualify annotes clusters, generated from PepMatch, according to gff annotation files.
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33
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34 **Integrated by**
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35
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36 Laetitia Guillot Cloarec
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37 PROTIM Biogenouest proteomics Core Facility, Rennes
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38 May,2016
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39
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40 ]]></help>
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41 <citations>
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42 <citation type="bibtex">
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43 @misc{renameTODO,
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44 author = {Protim Core facility},
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45 year = {2016},
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46 title = {ClustQualify},
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47 url = {protim.eu},
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48 }
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49 </citation>
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50 </citations>
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51 </tool>