Mercurial > repos > siwaa > redelac_stics_t

comparison redelacSticsTool.xml @ 24:0e673be917e3 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 596ce5faab821d6dcaf17fd56e002adc5be472fc"
author siwaa
date Tue, 01 Sep 2026 07:35:51 +0000
parents 3b44cb0a1e76
children 6839c9c8555e
comparison
equal deleted inserted replaced
23:3b44cb0a1e76 24:0e673be917e3
1 <tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.25"> 1 <tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.26">
2 <description>to run Stics for REDELAC</description> 2 <description>to run Stics for REDELAC</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forge.inrae.fr/redelac/redelac-toolbox/sticsrpacks:5337507635242b3ad0f3559a1a6b666512ecf002 4 <container type="singularity">docker://registry.forge.inrae.fr/redelac/redelac-toolbox/sticsrpacks:5337507635242b3ad0f3559a1a6b666512ecf002
5 </container> 5 </container>
6 </requirements> 6 </requirements>
7 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
8 <![CDATA[ 8 <![CDATA[
9 env &&
10 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" &&
11 unzip awscliv2.zip &&
12 ./aws/install --update -i ~/.local/aws-cli -b ~/.local/bin &&
13 export PATH=\${HOME}/.local/bin:\${PATH} &&
14 aws --version &&
9 #if $additional: 15 #if $additional:
10 additional=${additional} && 16 additional=${additional} &&
11 #else 17 #else
12 additional=noAdditionalPlantOrConfig && 18 additional=noAdditionalPlantOrConfig &&
13 #end if 19 #end if
14 #if $REDELAC.optim == 'optim': 20 #if $REDELAC.optim == 'optim':
15 parallel=${$REDELAC.parallel} && 21 parallel=${$REDELAC.parallel} &&
16 #else 22 #else
17 parallel=sequential && 23 parallel=sequential &&
18 #end if 24 #end if
19 bash $__tool_directory__/redelacSticsTool.bash ${REDELAC.optim} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress} ${outputsOnly} ${Scenario} ${SimulationResults} ${SuccessionPlan} ${outpuType} 25 bash $__tool_directory__/redelacSticsTool.bash ${REDELAC.optim} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress} ${outputsOnly} ${Scenario} ${SimulationResults} ${SuccessionPlan} ${outpuType} ${S3.S3} s3://${Bucket}/${objectPath}
20 ]]> 26 ]]>
21 </command> 27 </command>
22 <inputs> 28 <inputs>
23 <param name="Scenario" type="text" value="scenarioName" label="Scenario Name"/> 29 <param name="Scenario" type="text" value="scenarioName" label="Scenario Name"/>
24 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/> 30 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
42 <param name="outpuType" type="select" label="To choose the outpuType of results (rds+csv, parquet, both)"> 48 <param name="outpuType" type="select" label="To choose the outpuType of results (rds+csv, parquet, both)">
43 <option value="parquet">parquet</option> 49 <option value="parquet">parquet</option>
44 <option value="rds+csv">rds+csv</option> 50 <option value="rds+csv">rds+csv</option>
45 <option value="both" selected="true">both</option> 51 <option value="both" selected="true">both</option>
46 </param> 52 </param>
53 <conditional name="S3">
54 <param name="S3" type="boolean" checked="true" truevalue="ok" falsevalue="ko" label="To store directly on a Tenant"/>
55 <when value="ok">
56 <param name="objectPath" type="text" value="Simulations-stics/sous-territoires/PDF/ICHEC-EC-EARTH" label="a path to the object"/>
57 <param name="Bucket" type="text" value="dairyfit-donnees-produites" label="the bucket where to store"/>
58 </when>
59 <when value="ko">
60 </when>
61 </conditional>
47 </inputs> 62 </inputs>
48 <outputs> 63 <outputs>
49 <data format="zip" name="SimulationResults" 64 <data format="zip" name="SimulationResults"
50 label="SticsOnResults"> 65 label="SticsOnResults">
66 <filter>S3.S3 == False</filter>
51 </data> 67 </data>
52 <data format="zip" name="GeneratedWorkspace" 68 <data format="zip" name="GeneratedWorkspace"
53 label="GeneratedWorkspace$"> 69 label="GeneratedWorkspace$">
54 <filter>outputsOnly == False</filter> 70 <filter>outputsOnly == False</filter>
55 </data> 71 </data>