Mercurial > repos > siwaa > redelac_stics_g

comparison redelacSticsInputGenerator.xml @ 0:c7d424481b03 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac"
author siwaa
date Wed, 07 Jun 2023 06:08:27 +0000
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1 <tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.0">
2 <description>to run generate Stics Inputs for REDELAC</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 -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 unzip ${Climat} -d TMPbis &&
15 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
16 cp ${USMs} JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
17 cp ${Tec} JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
18 cp ${Ini} JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
19 cp ${Station} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
20 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
21 Rscript --verbose $__tool_directory__/redelacSticsInputGenerator.R &&
22 rm WS/1* &&
23 mv WS \$WSname &&
24 zip -r \$WSname \$WSname &&
25 cp \$WSname.zip ${GeneratedWorkspace}
26 ]]>
27 </command>
28 <inputs>
29 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
30 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>
31 <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
32 <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
33 <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
34 <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
35 </inputs>
36 <outputs>
37 <data format="zip" name="GeneratedWorkspace"
38 label="Stics generated Workspace">
39 </data>
40 </outputs>
41 <tests>
42 </tests>
43 <help>
44 *The usage of this tool is restricted to the user of the stics_authorized group.*
45
46 *To be granted, apply to the Project Stics Team and then request to SIWAA*
47
48 Documentation
49 -------------
50 A tool to generate Stics Inputs according to a plan for REDELAC
51
52 Credits
53 -------
54 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
55 - Stics Site: https://www6.paca.inra.fr/stics_eng
56 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
57 - Copyright: INRAE
58 </help>
59 </tool>