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1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.0">
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2 <description>To run the CarboSeq simulator</description>
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3 <requirements>
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4 <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/csopralibs_dev:paralleltoparallelly</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 bash -e -c "mkdir inputs &&
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8 unzip -d input ${input} &&
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9 set -a ;source /usr/local/src/myscripts/.env &&
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10 export CARBOSEQPREPROCESSOR_INPUT_DIR=\$(realpath -s input)
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11 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
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12 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r &&
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13 cd output &&
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14 zip -r output.zip * &&
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15 cp output.zip ${output}"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
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20 </inputs>
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21 <outputs>
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22 <data format='zip' name="output" label="CarboSeq output (zip)"/>
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23 </outputs>
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24 <tests>
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25 </tests>
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26 <help>
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27 the CarboSeq CarboseqSimulator tool
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28 ===================================
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29
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30 credits
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31 -------
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32 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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33 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
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34 - Copyright: INRAE
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35 </help>
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36 </tool>
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