<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.1">
  <description>to run generate Stics Inputs for REDELAC</description>
  <requirements>
    <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_test:10.0.0</container>
  </requirements>
  <command detect_errors="aggressive">
    <![CDATA[ 
	     cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . &&
	     rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
             cp -r $__tool_directory__/config JavaSTICS-1.5.1-STICS-10.0.0 &&
	     unzip ${Workspace} -d TMP &&
             export WSname=\$(ls TMP) &&
	     mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
             cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
             cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
	     unzip ${Climat} -d TMPbis &&
             mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
	     cp ${USMs} JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
	     cp ${Tec} JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
	     cp ${Ini} JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
	     cp ${Station} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
	     cd JavaSTICS-1.5.1-STICS-10.0.0 &&
	     Rscript --verbose $__tool_directory__/redelacSticsInputGenerator.R &&
             rm WS/1* &&
             mv WS \$WSname &&
	     zip -r \$WSname \$WSname &&
	     cp \$WSname.zip ${GeneratedWorkspace}
     ]]>
  </command>
  <inputs>
    <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
    <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>    
    <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
    <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
    <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
    <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
    <param name="Tag" type="text" value="" label="Outputs tag"/>
  </inputs>
  <outputs>
    <data format="zip" name="GeneratedWorkspace"
          label="GeneratedWorkspace${Tag}">
    </data>
  </outputs>
  <tests>
  </tests>
  <help>
*The usage of this tool is restricted to the user of the stics_authorized group.*

*To be granted, apply to the Project Stics Team and then request to SIWAA*

Documentation
-------------
A tool to generate Stics Inputs according to a plan for REDELAC

Credits
-------
-  Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
-  Stics Site: https://www6.paca.inra.fr/stics_eng
-  Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
-  Copyright: INRAE
  </help>
</tool>