<tool id="CarboSeqRunRothC" name="CarboSeqRunRothC" version="1.0.0">
  <description>To run the RothC simulator</description>
  <requirements>
    <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/record-projet-carboseq/testcaserothc:image-rothc-1.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
  bash -e -c "cp -r /work/csopralibs . &&
  cp ${simulation_data} CsopraAIALInTestCase.RData &&
  cp ${climat_data} csopralibs/data/Csopra/Climat_Csopra/CSOPRA_CLIMAT_MOIS_SAFRAN_2416.txt &&
  cp /work/csopralibs/scripts/R/testCaseRothC.r testCaseRothC.r &&
  sed -i 's/source(\"~\/\.Rpro/homeS <- \".\" #source(\"~\/\.Rpro/' testCaseRothC.r &&
  sed -i 's/setwd(homeS/setwd(getwd()/' testCaseRothC.r  &&
  sed -i 's/load(\"~\/tmp/load(\"\./' testCaseRothC.r &&
  R -e \"source('./testCaseRothC.r', echo=TRUE)\" > ${log} &&
  cp Rplots.pdf ${plot}"
    ]]>
  </command>
  <inputs>
    <param name="simulation_data" type="data" format="rdata" label="CarboSeq simulations data (rdata file)"/>
    <param name="climat_data" type="data" format="txt" label="CarboSeq climat data (txt file)"/>
  </inputs>
<outputs>
  <data format='txt' name="log" label="CarboSeq RothC log"/>
  <data format='pdf' name="plot" label="CarboSeq plot"/>
</outputs>
<tests>
  <test>
    <param name="simulation_data" value="inputs/Galaxy1-CarboSeq_simulations_data.rdata" ftype="rdata" />
    <param name="climat_data" value="inputs/CSOPRA_CLIMAT_MOIS_SAFRAN_2416.txt" ftype="txt" />
    <output name="plot">
    <assert_contents>
      <has_size value="27045" delta="100" />
    </assert_contents>
    </output>
    <output name="log">
      <assert_contents>
      <has_line line="> simTrial$runner$run()" />
    </assert_contents>
    </output>
  </test>

</tests>
<help>
the CarboSeqGetData tool
========================

credits
-------

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