Mercurial > repos > siwaa > redelac_stics_sim
comparison REDELACparallelSticsRsequence-10.0.xml @ 0:21e91d3b7068 draft
"planemo upload for repository https://forgemia.inra.fr/redelac"
| author | siwaa |
|---|---|
| date | Thu, 01 Jun 2023 09:13:11 +0000 |
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| -1:000000000000 | 0:21e91d3b7068 |
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| 1 <tool id="REDELACparallelSticsRsequence-10.0.0" name="redelacparallelsticsrsequence-10.0.0" version="1.0.0"> | |
| 2 <description>to run sequences paralelly 4 REDELAC[Stics-10.0.0]</description> | |
| 3 <requirements> | |
| 4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_redelac:10.0.0</container> | |
| 5 </requirements> | |
| 6 <command detect_errors="aggressive"> | |
| 7 <![CDATA[ | |
| 8 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . && | |
| 9 unzip ${WorkSpace} -d TMP && | |
| 10 export WSname=\$(ls TMP) && | |
| 11 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS && | |
| 12 cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv && | |
| 13 cd JavaSTICS-1.5.1-STICS-10.0.0 && | |
| 14 Rscript --verbose $__tool_directory__/REDELACparallelSticsRsequence.R && | |
| 15 mv WS \$WSname && | |
| 16 zip -r \$WSname \$WSname && | |
| 17 cp \$WSname.zip ${SimulatedWorkspace} && | |
| 18 cp results.RData ${SimulationResults} | |
| 19 ]]> | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/> | |
| 23 <param name="SuccessionPlan" type="data" format="csv" label="Select a plan (xlsx)"/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="zip" name="SimulatedWorkspace" | |
| 27 label="Stics simulated Workspace"> | |
| 28 </data> | |
| 29 <data format="rdata" name="SimulationResults" | |
| 30 label="Stics simulations results"> | |
| 31 </data> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 </tests> | |
| 35 <help> | |
| 36 *The usage of this tool is restricted to the user of the stics_authorized group.* | |
| 37 | |
| 38 *To be granted, apply to the Project Stics Team and then request to SIWAA* | |
| 39 | |
| 40 Documentation | |
| 41 ------------- | |
| 42 A tool to simulate stics rotation paralelly | |
| 43 | |
| 44 Credits | |
| 45 ------- | |
| 46 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team | |
| 47 - Stics Site: https://www6.paca.inra.fr/stics_eng | |
| 48 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr | |
| 49 - Copyright: INRAE | |
| 50 </help> | |
| 51 </tool> |