Mercurial > repos > siwaa > carboseq_s

annotate carboseqSimulator.xml @ 4:a069fc43b0b1 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty"
author siwaa
date Fri, 23 Aug 2024 13:19:04 +0000
parents d753f3430970
children f9183e245cdb
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a069fc43b0b1 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty"
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1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.11">
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2 <description>To run the CarboSeq simulator</description>
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3 <requirements>
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a069fc43b0b1 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty"
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4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwa</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 (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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8 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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9 bash -e -c "mkdir output &&
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10 unzip -d input ${input} &&
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a069fc43b0b1 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty"
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11 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
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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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12 cp output/* ${output}"
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
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17 </inputs>
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18 <outputs>
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19 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
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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="input" value="input/40Sites.zip" ftype="zip" />
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24 <output name="output" ftype="rdata" >
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25 <assert_contents>
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26 <has_size value="38654" negate="false" />
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27 <has_size value="0" negate="true" />
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28 </assert_contents>
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29 </output>
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30 </test>
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31 </tests>
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32 <help>
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33 the CarboSeq CarboseqSimulator tool
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34 ===================================
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35
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36 credits
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37 -------
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38 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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39 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
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40 - Copyright: INRAE
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41 </help>
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42 </tool>