<tool id="subSelect" name="subSelect" version="1.0.1">
  <description>netcdf spatial subselection</description>
  <requirements>
    <container type="singularity">docker://registry.forge.inrae.fr/dairyfit/lot1/chaine_traitement_indicateur:latest
    </container>
  </requirements>
  <command detect_errors="aggressive">
    <![CDATA[
	     mkdir -p VariableInputFolder/dummyFolder areaFolder VariableOutputFolder;
	     cp $climateModelVariable VariableInputFolder/dummyFolder/$climateModelVariable.name;
	     cd areaFolder;
	     tar -xvpf $area;
	     shpFile=\$(ls | grep shp);
	     cd ..;
	     conda run --no-capture-output -n dairyfit
	     python /data/1_subselect_Bretagne.py
             --input_dir VariableInputFolder
             --shapefile areaFolder/\$shpFile
	     --counties "$counties"
             --output_dir VariableOutputFolder;
	     cp \$(find VariableOutputFolder -type f) $climateVar
     ]]>
  </command>
  <inputs>
    <param name="selecTag" type="text" value="" label="Selection Name"/>
    <param name="climateModelVariable" type="data" format="netcdf" label="Select a climate model variable file (nc file)"/>
    <param name="area" type="data" format="tgz" label="Select a flat archive of a area shapeFile folder (tgz file)"/>
    <param name="counties" type="text" value="Côtes-d'Armor Finistère Ille-et-Vilaine Morbihan Loire-Atlantique Mayenne Sarthe Manche" label="List of counties" sanitize="False"/>
  </inputs>
  <outputs>
    <data format="netcdf" name="climateVar"
          label="${selecTag}${climateModelVariable.name}">
    </data>
  </outputs>
    <help>
Documentation
-------------
A tool to select a sub area of a netcddf file accordind to a shape file

Credits
-------
-  Wrapped Tool Author: Renan Le Roux renan.le-roux@inrae.fr
-  Site: https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox
-  Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
-  tool Site : https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox
-  Copyright: INRAE
  </help>
</tool>