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diff redelacSticsTool.xml @ 0:7f8f474a7bd7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
author siwaa
date Tue, 06 Feb 2024 09:21:00 +0000
parents
children ed9c49c6c6e1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/redelacSticsTool.xml	Tue Feb 06 09:21:00 2024 +0000
@@ -0,0 +1,242 @@
+<tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.0">
+  <description>to run Stics for REDELAC</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:1cadd3c67d29b07acb658836292f286e62922c5b</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 == 'yes'</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="optim" value="false" ftype="boolean" />
+      <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
+      <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />    
+      <param name="USMs" value="input/USMsSheet.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/StationsSheet.csv" ftype="csv"/>
+      <output name="GeneratedWorkspace" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
+	  </has_archive_member>
+	</assert_contents>	  
+      </output>
+    </test>
+    <test>
+      <param name="parallel" value="false" ftype="boolean" />
+      <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
+      <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />    
+      <param name="USMs" value="input/USMsSheet.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/StationsSheet.csv" ftype="csv"/>
+      <output name="GeneratedWorkspace" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
+	  </has_archive_member>
+	</assert_contents>	  
+      </output>
+    </test>
+    <test>
+      <param name="parallel" value="true" ftype="boolean" />
+      <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
+      <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />    
+      <param name="USMs" value="input/USMsSheet.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/StationsSheet.csv" ftype="csv"/>
+      <output name="GeneratedWorkspace" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
+	  </has_archive_member>
+	</assert_contents>	  
+      </output>
+    </test>
+    <test>
+      <param name="compress" value="false" ftype="boolean" />
+      <param name="parallel" value="true" ftype="boolean" />
+      <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
+      <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />    
+      <param name="USMs" value="input/USMsSheet.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/StationsSheet.csv" ftype="csv"/>
+      <output name="GeneratedWorkspace" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
+	  </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>