Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.xml @ 2:c60c25773642 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/redelac commit 823237fb6720db009ad2ca7e113de353abde6c30"
author siwaa
date Mon, 19 Jun 2023 17:25:39 +0000
parents c7d424481b03
children e344100f3354
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
1 <tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.0">
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
2 <description>to run generate Stics Inputs for REDELAC</description>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
3 <requirements>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics:10.0.0</container>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
5 </requirements>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
6 <command detect_errors="aggressive">
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
7 <![CDATA[
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
8 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
9 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
10 cp -r $__tool_directory__/config JavaSTICS-1.5.1-STICS-10.0.0 &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
11 unzip ${Workspace} -d TMP &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
12 export WSname=\$(ls TMP) &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
13 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
14 unzip ${Climat} -d TMPbis &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
15 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
16 cp ${USMs} JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
17 cp ${Tec} JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
18 cp ${Ini} JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
19 cp ${Station} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
20 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
21 Rscript --verbose $__tool_directory__/redelacSticsInputGenerator.R &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
22 rm WS/1* &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
23 mv WS \$WSname &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
24 zip -r \$WSname \$WSname &&
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
25 cp \$WSname.zip ${GeneratedWorkspace}
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
26 ]]>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
27 </command>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
28 <inputs>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
29 <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
30 <param name="Climat" type="data" format="zip" label="Select a climat scenario (zip file)"/>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
31 <param name="USMs" type="data" format="csv" label="Select the USMs sheet (csv)"/>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
32 <param name="Tec" type="data" format="csv" label="Select the Tec sheet (csv)"/>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
33 <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
34 <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
35 </inputs>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
36 <outputs>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
37 <data format="zip" name="GeneratedWorkspace"
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
38 label="Stics generated Workspace">
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
39 </data>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
40 </outputs>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
41 <tests>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
42 </tests>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
43 <help>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
44 *The usage of this tool is restricted to the user of the stics_authorized group.*
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
45
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
46 *To be granted, apply to the Project Stics Team and then request to SIWAA*
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
47
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
48 Documentation
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
49 -------------
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
50 A tool to generate Stics Inputs according to a plan for REDELAC
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
51
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
52 Credits
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
53 -------
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
54 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
55 - Stics Site: https://www6.paca.inra.fr/stics_eng
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
56 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
57 - Copyright: INRAE
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
58 </help>
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
59 </tool>