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11
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1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.8">
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0
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2 <description>To run the CarboSeq simulator</description>
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3 <requirements>
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7
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4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop</container>
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0
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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11
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7 mkdir data &&
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8 cp $__tool_directory__/ontology.owl data &&
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9 cp -r $__tool_directory__/config_mappers . &&
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10 cp $__tool_directory__/semantifier.jar . &&
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7
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11 (env | grep DOCKER_IMAGE) &&
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12 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
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5
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13 bash -e -c "mkdir output &&
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0
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14 unzip -d input ${input} &&
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2
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15 mkdir tmp &&
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5
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16 export TMPDIR="\${PWD}/tmp" &&
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11
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17 Rscript $__tool_directory__/run.r --url=https://localhost:8585/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
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1
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18 mv output/* ${output}"
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0
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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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1
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25 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
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0
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26 </outputs>
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27 <tests>
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28 </tests>
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29 <help>
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30 the CarboSeq CarboseqSimulator tool
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31 ===================================
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32
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33 credits
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34 -------
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35 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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36 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
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37 - Copyright: INRAE
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38 </help>
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39 </tool>
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