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comparison redelacSticsSimulator.xml @ 2:ea8e91473dc8 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
author siwaa
date Fri, 23 Jun 2023 10:17:27 +0000
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children fa8e742b197b
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1:be10e3fb6e64 2:ea8e91473dc8
1 <tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.1">
2 <description>to run sequences paralelly [Stics-10.0.0]</description>
3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics: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 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 ${SimulationResults}
21 ]]>
22 </command>
23 <inputs>
24 <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
25 <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
26 <param name="Tag" type="text" value="" label="Outputs tag"/>
27 </inputs>
28 <outputs>
29 <data format="zip" name="SimulatedWorkspace"
30 label="SticsSimulatedWorkspace${Tag}">
31 </data>
32 <data format="rdata" name="SimulationResults"
33 label="SticsOnResults${Tag}">
34 </data>
35 </outputs>
36 <tests>
37 </tests>
38 <help>
39 *The usage of this tool is restricted to the user of the stics_authorized group.*
40
41 *To be granted, apply to the Project Stics Team and then request to SIWAA*
42
43 Documentation
44 -------------
45 A tool to simulate stics rotation paralelly
46
47 Credits
48 -------
49 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
50 - Stics Site: https://www6.paca.inra.fr/stics_eng
51 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
52 - Copyright: INRAE
53 </help>
54 </tool>