<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.0">
  <description>To run the CarboSeq simulator</description>
  <requirements>
    <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/csopralibs_dev:paralleltoparallelly</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
  bash -e -c "mkdir inputs &&
  unzip -d input ${input} &&
  set -a ;source /usr/local/src/myscripts/.env &&
  export CARBOSEQPREPROCESSOR_INPUT_DIR=\$(realpath -s input)
  export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
  Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r &&
  cd output &&
  zip -r output.zip * &&
  cp output.zip ${output}"
    ]]>
  </command>
  <inputs>
    <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
  </inputs>
<outputs>
  <data format='zip' name="output" label="CarboSeq output (zip)"/>
</outputs>
<tests>
</tests>
<help>
the CarboSeq CarboseqSimulator tool
===================================

credits
-------
-  Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
-  Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
-  Copyright: INRAE
</help>
</tool>