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8
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1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.7">
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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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8
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7 (java -Dquarkus.http.port=8282 -jar $__tool_directory__/semantifier.jar &) &&
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8 env &&
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7
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9 (env | grep DOCKER_IMAGE) &&
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10 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
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5
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11 bash -e -c "mkdir output &&
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0
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12 unzip -d input ${input} &&
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2
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13 mkdir tmp &&
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5
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14 export TMPDIR="\${PWD}/tmp" &&
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8
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15 Rscript $__tool_directory__/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&&
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1
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16 mv output/* ${output}"
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0
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
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21 </inputs>
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22 <outputs>
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1
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23 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
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0
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24 </outputs>
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25 <tests>
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26 </tests>
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27 <help>
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28 the CarboSeq CarboseqSimulator tool
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29 ===================================
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30
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31 credits
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32 -------
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33 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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34 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
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35 - Copyright: INRAE
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36 </help>
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37 </tool>
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