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"planemo upload for repository https://forgemia.inra.fr/redelac commit dad4c83e555d8c94c7bd3442c9b4771af97a0462"
author siwaa
date Tue, 23 Sep 2025 10:46:12 +0000
parents cbd23f8906db
children
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<tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.14">
  <description>to run Stics for REDELAC</description>
  <requirements>
    <container type="singularity">docker://registry.forge.inrae.fr/redelac/redelac-toolbox/sticsrpacks:f1b039d1eec2c48260f2a3531b9f821948f9cad7</container>
  </requirements>
  <command detect_errors="aggressive">
    <![CDATA[
	     #if $additional:
                additional=${additional} &&
	     #else
                additional=noAdditionalPlantOrConfig &&
             #end if
	     #if $REDELAC.optim == 'optim':
                parallel=${$REDELAC.parallel} &&
             #else
                parallel=sequential &&
             #end if
	        bash $__tool_directory__/redelacSticsTool.bash ${REDELAC.optim} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress} ${outputsOnly} ${Scenario} ${SimulationResults} ${SuccessionPlan}
     ]]>
  </command>
  <inputs>
    <param name="Scenario" type="text" value="scenarioName" label="Scenario Name"/>
    <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
    <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>    
    <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
    <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
    <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
    <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
    <param name="additional" type="data" optional="true" format="zip" label="[optional] Select a zipped archive with folder plant (and or) config (zip file)"/>
    <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
    <conditional name="REDELAC">
      <param name="optim" type="boolean" checked="true" truevalue="optim" falsevalue="noptim" label="To speed up the xml2txt conversion process by generating file only once"/>
      <when value="optim">
	<param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential" label="To parallelize the xml2txt conversion process" />
      </when>
	<when value="noptim">
      </when>
    </conditional>
    <param name="outputsOnly" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="To get results only"/>
    <param name="compress" type="boolean" checked="true" truevalue="-6" falsevalue="-0" label="To compress or not the output(compressing does slow down the job)"/>
  </inputs>
  <outputs>
    <data format="zip" name="SimulationResults"
          label="SticsOnResults">
    </data>
    <data format="zip" name="GeneratedWorkspace"
          label="GeneratedWorkspace$">
              <filter>outputsOnly == False</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="compress" value="false" ftype="boolean" />
      <param name="outputsOnly" value="false" ftype="boolean" />
      <param name="optim" value="true" ftype="boolean" />
      <param name="parallel" value="true" ftype="boolean" />
      <param name="Workspace" value="input/rot1_3.zip" ftype="zip" />
      <param name="Climat" value="input/flat_cnrm-cm5-aladin63_rcp2.6.zip" ftype="zip" />   
      <param name="USMs" value="input/USMsSheetExp.csv" ftype="csv" />
      <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
      <param name="Ini" value="input/IniSheet.csv" ftype="csv" />
      <param name="Station" value="input/StationsSheetExp.csv" ftype="csv" />
      <param name="additional" value="input/conf_rot1_3.zip" ftype="zip" />	  
      <param name="SuccessionPlan" value="input/successionsSheetExp.csv" ftype="csv" />
      <output name="GeneratedWorkspace" ftype="zip" >
	<assert_contents>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1973-PP1\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1973-PP1" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1974-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1974-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1975-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1975-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-1976-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-1976-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-1977-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-1977-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2000-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2000-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2001-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2001-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2002-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2002-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2003-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2003-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2004-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2004-PP" />
	  </has_archive_member>
	</assert_contents>	  
      </output>
      <output name="SimulationResults" ftype="zip" >
	<assert_contents>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/outputs-3-806_1893-637_NPP1-scenarioName.rds">
	    <has_size value="0" negate="true" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/outputs-3-806_1893-638_NPP1-scenarioName.rds">
	    <has_size value="0" negate="true" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/report-3-806_1893-637_NPP1-scenarioName.csv">
	    <has_n_lines n="133" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/report-3-806_1893-638_NPP1-scenarioName.csv">
	    <has_n_lines n="133" />
	  </has_archive_member>
	</assert_contents>	  	  
      </output>	  
    </test>
    <test>
      <param name="compress" value="false" ftype="boolean" />
      <param name="outputsOnly" value="false" ftype="boolean" />
      <param name="optim" value="true" ftype="boolean" />
      <param name="parallel" value="false" ftype="boolean" />
      <param name="Workspace" value="input/rot1_3.zip" ftype="zip" />
      <param name="Climat" value="input/flat_cnrm-cm5-aladin63_rcp2.6.zip" ftype="zip" />   
      <param name="USMs" value="input/USMsSheetExp.csv" ftype="csv" />
      <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
      <param name="Ini" value="input/IniSheet.csv" ftype="csv" />
      <param name="Station" value="input/StationsSheetExp.csv" ftype="csv" />
      <param name="additional" value="input/conf_rot1_3.zip" ftype="zip" />	  
      <param name="SuccessionPlan" value="input/successionsSheetExp.csv" ftype="csv" />
      <output name="GeneratedWorkspace" ftype="zip" >
	<assert_contents>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1973-PP1\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1973-PP1" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1974-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1974-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1975-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1975-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-1976-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-1976-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-1977-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-1977-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2000-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2000-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2001-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2001-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2002-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2002-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2003-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2003-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2004-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2004-PP" />
	  </has_archive_member>
	</assert_contents>	  
      </output>
            <output name="SimulationResults" ftype="zip" >
	<assert_contents>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/outputs-3-806_1893-637_NPP1-scenarioName.rds">
	    <has_size value="0" negate="true" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/outputs-3-806_1893-638_NPP1-scenarioName.rds">
	    <has_size value="0" negate="true" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/report-3-806_1893-637_NPP1-scenarioName.csv">
	    <has_n_lines n="133" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/report-3-806_1893-638_NPP1-scenarioName.csv">
	    <has_n_lines n="133" />
	  </has_archive_member>
	</assert_contents>	  	  
      </output>	  
    </test>
    <test>
      <param name="compress" value="false" ftype="boolean" />
      <param name="outputsOnly" value="false" ftype="boolean" />
      <param name="optim" value="false" ftype="boolean" />
      <param name="Workspace" value="input/rot1_3.zip" ftype="zip" />
      <param name="Climat" value="input/flat_cnrm-cm5-aladin63_rcp2.6.zip" ftype="zip" />   
      <param name="USMs" value="input/USMsSheetExp.csv" ftype="csv" />
      <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
      <param name="Ini" value="input/IniSheet.csv" ftype="csv" />
      <param name="Station" value="input/StationsSheetExp.csv" ftype="csv" />
      <param name="additional" value="input/conf_rot1_3.zip" ftype="zip" />	  
      <param name="SuccessionPlan" value="input/successionsSheetExp.csv" ftype="csv" />
      <output name="GeneratedWorkspace" ftype="zip" >
	<assert_contents>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1973-PP1\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1973-PP1" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1974-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1974-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-NA-1975-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-NA-1975-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-1976-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-1976-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-1977-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-1977-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2000-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2000-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2001-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2001-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2002-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2002-PP" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2003-PPorg\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2003-PPorg" />
	  </has_archive_member>
	  <has_archive_member path="rot1_3\/txt_files\/806_1893-637_NPP1-1-3-PP-ref-2004-PP\/new_travail.usm">
	    <has_text text="806_1893-637_NPP1-1-3-PP-ref-2004-PP" />
	  </has_archive_member>
	</assert_contents>	  
      </output>
            <output name="SimulationResults" ftype="zip" >
	<assert_contents>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/outputs-3-806_1893-637_NPP1-scenarioName.rds">
	    <has_size value="0" negate="true" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/outputs-3-806_1893-638_NPP1-scenarioName.rds">
	    <has_size value="0" negate="true" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/report-3-806_1893-637_NPP1-scenarioName.csv">
	    <has_n_lines n="133" />
	  </has_archive_member>
	  <has_archive_member path="analyse_simulations_STICS\/1\/3\/report-3-806_1893-638_NPP1-scenarioName.csv">
	    <has_n_lines n="133" />
	  </has_archive_member>
	</assert_contents>	  	  
      </output>	  
    </test>
  </tests>
  <help>
*The usage of this tool is restricted to the user of the redelac_authorized group.*

*To be granted, apply to the REDELAC Project 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>