<tool id="CarboSeqRunSim" name="CarboSeqRunSim" version="1.1.0">
  <description>To run the simulator</description>
  <requirements>
    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.1.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
  bash -e -c "mkdir inputs &&
  cp ${meteo_data} inputs/meteo.csv &&
  cp ${crop_data} inputs/crop.csv &&
  cp ${soil_data} inputs/soil.csv &&
  mkdir output &&
  export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
  export CSVMAPPER_INPUT_DIR=\$(realpath -s inputs) &&
  #if $id_pairs
  export CSOPRALIBS_ID_IDSUCC_CSV_FILE=${id_pairs} &&
  #end if
  export CSOPRALIBS_SIM_PARAMS_IMPLEMENTATION=${simulator} &&
  Rscript /usr/local/src/myscripts/usercases/run-sim/run.r &&
  cp output/SimulationSOCResults.RData ${run_output}"
    ]]>
  </command>
  <inputs>
    <param name="simulator" type="select" label="Simulator">
      <option value="rothC" selected="true">rothC</option>
      <option value="soilr">soilr</option>
    </param>
    <param name="meteo_data" type="data" format="csv" label="Meteo data (csv file)"/>
    <param name="crop_data" type="data" format="csv" label="Crop data (csv file)"/>
    <param name="soil_data" type="data" format="csv" label="Soil data (csv file)"/>
    <param name="id_pairs" type="data" optional="true" format="csv" label="Id pairs (csv file)"/>
  </inputs>
<outputs>
  <data format='rdata' name="run_output" label="Simulation SOC Results"/>
</outputs>
<tests>
  <test>    
    <param name="simulator" value="rothC" />
    <param name="id_pairs" value="outputs/id-idSucc-pairs.csv" ftype="csv"/>
    <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" />
    <param name="crop_data" value="inputs/client.files/crop.csv" ftype="csv" />
    <param name="soil_data" value="inputs/client.files/soil.csv" ftype="csv" />
    <output name="run_output">
    <assert_contents>
      <has_size value="5462" delta="100" />
    </assert_contents>
    </output>
  </test>
</tests>
<help>
the CarboSeq run-sim  tool
==========================

credits
-------

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