annotate clust_to_gff.xml @ 1:8ef59dde4389 draft default tip

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper commit 040d09319fb0f43fafb1d3ebd99af41bce0f6bfd
author genouest
date Thu, 18 Jul 2024 10:26:15 +0000
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8ef59dde4389 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper commit 040d09319fb0f43fafb1d3ebd99af41bce0f6bfd
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1 <tool id="peptimapper_clust_to_gff" name="ClustToGFF" version="2.1">
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2 <description>add clusters locations into GFF files to be integrated into a genome viewer</description>
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3 <requirements>
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4 <container type="docker">dockerprotim/peptimapper@sha256:d3eb807d7d5aa155f7b39d05a47420e0a0a9191d5fa867b6ca1be763f8a23bf1</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 unzip '${gffdir}' -d gff &&
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8 mkdir "outputdir" &&
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9 LXClust2Gff gff/* outputdir '${clustersfile}' &&
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10 mv *.gff outputdir/ &&
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11 zip -r outputdir2 outputdir/* &&
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12 mv outputdir2.zip '${gfffiles}'
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13 ]]></command>
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14 <inputs>
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15 <param name="clustersfile" type="data" format="txt" label="Clusters file" help="Clusters file generated by PepMatch" />
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16 <param name="gffdir" type="data" format="zip" label="GFF files repository" help="Zipped repository containing all organism GFF files" />
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17 </inputs>
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18 <outputs>
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19 <data name="gfffiles" format="zip" label="GFF files including clusters locations" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="clustersfile" value="clusttogff/Gamete.5.3.2.5000.clust"/>
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24 <param name="gffdir" value="clusttogff/gff3_files_repository.zip"/>
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25 <output name="gfffiles" file="clusttogff/out.zip" compare="sim_size"/>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 **Description**
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30
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31 ClustToGFF : run LXClust2Gff from the "peptimapper" docker.
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32 ClustToGFF adds clusters locations, generated by PepMatch, into GFF annotation files to be integrated into a genome viewer.
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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 July,2017
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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 = {2017},
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45 title = {ClustToGFF},
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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>