Mercurial > repos > siwaa > redelac_stics_s

comparison redelacSticsSimulator.xml @ 6:41f652e6616f draft

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"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
comparison
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5:fa8e742b197b 6:41f652e6616f
1 <tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.2"> 1 <tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.3">
2 <description>to run sequences paralelly [Stics-10.0.0]</description> 2 <description>to run sequences paralelly [Stics-10.0.0]</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics:10.0.0</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:28483bbc8a70159a36bccc30e2270284ea4388e3</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"> 6 <command detect_errors="aggressive">
7 <![CDATA[ 7 <![CDATA[
8 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . && 8 bash $__tool_directory__/redelacSticsSimulator.bash ${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${SuccessionPlan} ${SimulatedWorkspace} ${SimulationResults}
9 rm JavaSTICS-1.5.1-STICS-10.0.0/bin/stics_modulo &&
10 cp $__tool_directory__/stics_modulo JavaSTICS-1.5.1-STICS-10.0.0/bin &&
11 unzip -qq ${WorkSpace} -d TMP &&
12 export WSname=\$(ls TMP) &&
13 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
14 cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
15 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
16 Rscript --verbose $__tool_directory__/redelacSticsSimulator.R \${GALAXY_SLOTS:-2} &&
17 mv WS \$WSname &&
18 zip -qq -r \$WSname \$WSname &&
19 cp \$WSname.zip ${SimulatedWorkspace} &&
20 cp results.RData ${SimulationResults}
21 ]]> 9 ]]>
22 </command> 10 </command>
23 <inputs> 11 <inputs>
24 <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/> 12 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
25 <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/> 13 <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
26 <param name="Tag" type="text" value="" label="Outputs tag"/> 14 <param name="Tag" type="text" value="" label="Outputs tag"/>
15 <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/>
27 </inputs> 16 </inputs>
28 <outputs> 17 <outputs>
29 <data format="zip" name="SimulatedWorkspace" 18 <data format="zip" name="SimulatedWorkspace"
30 label="SticsSimulatedWorkspace${Tag}"> 19 label="SticsSimulatedWorkspace${Tag}">
31 </data> 20 </data>