<tool id="CarboSeqPrepareSim" name="CarboSeqPrepareSim" version="1.0.0">
  <description>To prepare the data for simulating</description>
  <requirements>
    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.0.0</container>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[
  bash -e -c "mkdir -p data/client.files &&
  cp ${meteo_data} data/client.files/meteo.csv &&
  cp ${crop_data} data/client.files/crop.csv &&
  cp ${soil_data} data/client.files/soil.csv &&
  mkdir -p data/mapping.files &&
  cp ${crop_mapping} data/mapping.files/crop.mapping.csv &&
  cp ${property_mapping} data/mapping.files/property.mapping.csv &&
  mkdir output &&
  export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
  cp /usr/local/src/myscripts/usercases/prepare-sim/run.r . &&
  Rscript run.r &&
  cp output/RothcPreparedRunnerResults.RData ${prepare_output}"
    ]]>
  </command>
  <inputs>
    <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="crop_mapping" type="data" format="csv" label="crop mapping (csv file)"/>
    <param name="property_mapping" type="data" format="csv" label="property mapping (csv file)"/>
  </inputs>
<outputs>
  <data format='rdata' name="prepare_output" label="Rothc Prepared Runner Results"/>
</outputs>
<tests>
  <test>
    <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" />
    <param name="crop_mapping" value="inputs/mapping.files/crop.mapping.csv" ftype="csv" />
    <param name="property_mapping" value="inputs/mapping.files/property.mapping.csv" ftype="csv"/>
    <output name="prepare_output">
    <assert_contents>
      <has_size value="5474" />
    </assert_contents>
    </output>
  </test>
</tests>
<help>
the CarboSeqPrepareSim 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>