<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.1">
  <description>to run sequences paralelly [Stics-10.0.0]</description>
  <requirements>
    <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics: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 JavaSTICS-1.5.1-STICS-10.0.0/bin/stics_modulo &&
             cp $__tool_directory__/stics_modulo JavaSTICS-1.5.1-STICS-10.0.0/bin &&
	     unzip -qq ${WorkSpace} -d TMP &&
             export WSname=\$(ls TMP) &&
	     mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
	     cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
	     cd JavaSTICS-1.5.1-STICS-10.0.0 &&
	     Rscript --verbose $__tool_directory__/redelacSticsSimulator.R \${GALAXY_SLOTS:-2}	&&
             mv WS \$WSname &&
	     zip -qq -r \$WSname \$WSname &&
	     cp \$WSname.zip ${SimulatedWorkspace} &&
	     cp results.RData ${SimulationResults}
     ]]>
  </command>
  <inputs>
    <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
    <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
    <param name="Tag" type="text" value="" label="Outputs tag"/>
  </inputs>
  <outputs>
    <data format="zip" name="SimulatedWorkspace"
          label="SticsSimulatedWorkspace${Tag}">
    </data>
    <data format="rdata" name="SimulationResults"
          label="SticsOnResults${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 simulate stics rotation paralelly

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>