<tool id="AZODYN" name="AZODYN crop models simulations" version="1.5.0">
  <description></description>
  <requirements>
    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:image-azodynsunflo-1.5</container>
  </requirements>
  <command detect_errors="aggressive">
    unzip ${input_meteo}; 
    dos2unix --allow-chown *
    dos2unix -n ${file_input} internal_inputAZODYN.csv;
    dos2unix -n ${file_outputs} internal_outputAZODYN.csv; 
    /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R ${crop_type} AZODYN internal_inputAZODYN.csv internal_outputAZODYN.csv \${GALAXY_SLOTS:-2}";
    zip temp_results.zip  simresults_*.txt;
    cp temp_results.zip ${simresults};
  </command>
  <inputs>
    <param name="crop_type" type="select"  label="Select crop to simulate">
      <option value="AzodynPea.vpz">Pea</option>
      <option value="AzodynWheat.vpz">Wheat</option>
      <option value="AzodynBarley.vpz">Barley</option>
      <option value="AzodynColza.vpz">Rapeseed</option>
    </param>
    <param name="input_meteo" type="data" format="zip" label="Wheater serie input files (zip file)"/>
    <param name="file_input" type="data" format="csv" label="Crop model input values"/>
    <param name="file_outputs" type="data" format="csv" label="Outputs to simulate"/>
  </inputs>
  <outputs>
    <data format="zip" name="simresults" />
  </outputs>
  <tests>
  <test>
    <param name="crop_type" value="AzodynPea.vpz" />
    <param name="input_meteo" value="inputs/AzodynPea_meteo.zip" ftype="zip" />
    <param name="file_input" value="inputs/AzodynPea_input.csv" ftype="csv" />
    <param name="file_outputs" value="inputs/AzodynPea_output.csv" ftype="csv" />
    <output name="simresults">
    <assert_contents>
      <has_archive_member path="simresults_LAI.txt">
	<has_text text="0;0;0;0" />
	<has_text text="0.02230323" />
      </has_archive_member>
      <has_archive_member path="simresults_MS.txt">
	<has_text text="0;0;0;0" />
	<has_text text="1.568" />
      </has_archive_member>
    </assert_contents>
    </output>
  </test>
</tests>
  <help><![CDATA[
AZODYN crop models simulations
==============================

Inputs:
-------

- Zip file of wheather series
- Input values of the crop model (1 simulation per row)
- Identification of the crop model output to simulate.

Outputs:
--------

- Zip file of the crop model simulation values (1 file per output)

Example:
--------

- Select 'Pea' as the crop model to use
- Copy to your history files 'AzodynPea_meteo.zip', 'AzodynPea_input.csv' and 'AzodynPea_output.csv' from the AZODYN shared dataset.
- Fill file names and choose the adequate number of cores.
- And then execute 

Credits:
--------

-  Author: Ronan Trépos ronan.trepos@inrae.fr
-  Wrapper Maintainer: Ronan Trépos ronan.trepos@inrae.fr
-  Tool Maintainer: Ronan Trépos ronan.trepos@inrae.fr
-  Copyright: INRAE]]>
  </help>
</tool>