Mercurial > repos > siwaa > redelac_stics_g

diff redelacSticsInputGenerator.xml @ 9:2a6d7d053ba7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
author siwaa
date Mon, 25 Sep 2023 16:25:51 +0000
parents 0625e6a639ea
children f707c2fb725b
line wrap: on
line diff
--- a/redelacSticsInputGenerator.xml	Wed Aug 30 08:23:12 2023 +0000
+++ b/redelacSticsInputGenerator.xml	Mon Sep 25 16:25:51 2023 +0000
@@ -1,12 +1,17 @@
-<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.2">
+<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.4">
   <description>to run generate Stics Inputs for REDELAC</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrfiles:9a2d54c0674a6b902299dd22fdd37c2f67509fa2</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:b782e0b7ce3af7e7a14a87ea750145ed1c2595a0</container>
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[
-	     bash $__tool_directory__/redelacSticsInputGenerator.bash ${IterUsmX} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} ${GeneratedWorkspace}
-     ]]>{
+	     #if str( $IterUsmX.IterUsmX ) == 'usmx_one_after_other':
+                parallel=${$IterUsmX.parallel} &&
+             #else
+                parallel=parallel &&
+             #end if
+	        bash $__tool_directory__/redelacSticsInputGenerator.bash ${IterUsmX.IterUsmX} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} ${GeneratedWorkspace}
+     ]]>
   </command>
   <inputs>
     <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
@@ -16,7 +21,14 @@
     <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"/>
-    <param name="IterUsmX" type="boolean" checked="true" truevalue="usmx_one_after_other" falsevalue="usmx_at_once"/>
+    <conditional name="IterUsmX">
+      <param name="IterUsmX" type="boolean" checked="true" truevalue="usmx_one_after_other" falsevalue="usmx_at_once"/>
+      <when value="usmx_one_after_other">
+	<param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/>
+      </when>
+	<when value="usmx_at_once">
+      </when>
+    </conditional>
   </inputs>
   <outputs>
     <data format="zip" name="GeneratedWorkspace"
@@ -25,6 +37,50 @@
   </outputs>
   <tests>
     <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" />