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annotate carboseqSimulator.xml @ 1:89c69fcbf561 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
author siwaa
date Fri, 09 Aug 2024 15:09:48 +0000
parents fb1b9308807f
children d78961e3f5ca
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.9">
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2 <description>To run the CarboSeq simulator</description>
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3 <requirements>
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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7 mkdir data &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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8 cp $__tool_directory__/ontology.owl data &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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9 cp -r $__tool_directory__/config_mappers . &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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10 cp $__tool_directory__/semantifier.jar . &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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11 (env | grep DOCKER_IMAGE) &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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12 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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13 bash -e -c "mkdir output &&
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14 unzip -d input ${input} &&
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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15 mkdir tmp &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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16 export TMPDIR="\${PWD}/tmp" &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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17 Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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18 cp output/* ${output}"
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
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23 </inputs>
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24 <outputs>
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25 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
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26 </outputs>
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27 <tests>
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28 <test>
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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29 <param name="input" value="input/40Sites.zip" ftype="zip" />
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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30 <output name="output" ftype="rdata" >
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31 <assert_contents>
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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32 <has_size value="1156" negate="false" />
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33 <has_size value="0" negate="true" />
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34 </assert_contents>
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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35 </output>
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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36 </test>
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37 </tests>
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38 <help>
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39 the CarboSeq CarboseqSimulator tool
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40 ===================================
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41
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42 credits
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43 -------
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44 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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45 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
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46 - Copyright: INRAE
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47 </help>
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48 </tool>