Mercurial > repos > siwaa > redelac_stics_s

diff redelacSticsSimulator.xml @ 6:41f652e6616f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/f8a7aebffe0c850bef03045efa3772aca6cd51c2/tools/REDELACSticsSimulator commit f8a7aebffe0c850bef03045efa3772aca6cd51c2-dirty"
author siwaa
date Tue, 26 Sep 2023 15:21:42 +0000
parents fa8e742b197b
children 2586f7dbcde1
line wrap: on
line diff
--- a/redelacSticsSimulator.xml	Mon Aug 21 15:47:50 2023 +0000
+++ b/redelacSticsSimulator.xml	Tue Sep 26 15:21:42 2023 +0000
@@ -1,29 +1,18 @@
-<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.2">
+<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.3">
   <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>
+    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:28483bbc8a70159a36bccc30e2270284ea4388e3</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}
+              bash $__tool_directory__/redelacSticsSimulator.bash ${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${SuccessionPlan} ${SimulatedWorkspace} ${SimulationResults}
      ]]>
   </command>
   <inputs>
-    <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
+    <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"/>
+    <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/>
   </inputs>
   <outputs>
     <data format="zip" name="SimulatedWorkspace"