Mercurial > repos > siwaa > redelac_stics_g

comparison redelacSticsInputGenerator.xml @ 5:4f8d87b9c246 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
author siwaa
date Tue, 04 Jul 2023 16:37:44 +0000
parents af7d9ca55205
children fb6f7d60508d
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4:af7d9ca55205 5:4f8d87b9c246
2 <description>to run generate Stics Inputs for REDELAC</description> 2 <description>to run generate Stics Inputs for REDELAC</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_test:10.0.0</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_test:10.0.0</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__/redelacSticsInputGenerator.bash $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} ${GeneratedWorkspace}
9 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
10 cp -r $__tool_directory__/config JavaSTICS-1.5.1-STICS-10.0.0 &&
11 unzip ${Workspace} -d TMP &&
12 export WSname=\$(ls TMP) &&
13 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
14 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
15 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
16 unzip ${Climat} -d TMPbis &&
17 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
18 cp ${USMs} JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
19 cp ${Tec} JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
20 cp ${Ini} JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
21 cp ${Station} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
22 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
23 Rscript --verbose $__tool_directory__/redelacSticsInputGenerator.R &&
24 rm WS/1* &&
25 mv WS \$WSname &&
26 zip -r \$WSname \$WSname &&
27 cp \$WSname.zip ${GeneratedWorkspace}
28 ]]> 9 ]]>
29 </command> 10 </command>
30 <inputs> 11 <inputs>
31 <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)"/>
32 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/> 13 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>