Mercurial > repos > siwaa > redelac

annotate parallelSticsRRotation-10.0.xml @ 0:e8b0d1d0797d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
author siwaa
date Tue, 21 Feb 2023 19:03:38 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
1 <tool id="parallelSticsRRotation-10.0.0" name="parallelsticsrrotation-10.0.0" version="1.0.0">
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
2 <description>to run rotation paralelly [Stics-10.0.0]</description>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
3 <requirements>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics:10.0.0</container>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
5 </requirements>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
6 <command detect_errors="aggressive">
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
7 <![CDATA[
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
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 . &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
9 unzip ${WorkSpace} -d TMP &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
10 mkdir WS &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
11 mv TMP/* WS/txt_files &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
12 cp ${RotationPlan} WS/rotationPlan.xlsx &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
13 mkdir config &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
14 Rscript --verbose $__tool_directory__/parallelSticsRRotation.R &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
15 zip -r WS WS &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
16 cp WS.zip ${SimulatedWorkspace} &&
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
17 cp results.RData ${SimulationResults}
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
18 ]]>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
19 </command>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
20 <inputs>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
21 <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
22 <param name="RotationPlan" type="data" format="xlsx" label="Select a plan (xlsx)"/>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
23 </inputs>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
24 <outputs>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
25 <data format="zip" name="SimulatedWorkspace"
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
26 label="Stics simulated Workspace">
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
27 </data>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
28 <data format="rdata" name="SimulationResults"
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
29 label="Stics simulations results">
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
30 </data>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
31 </outputs>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
32 <tests>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
33 </tests>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
34 <help>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
35 *The usage of this tool is restricted to the user of the stics_authorized group.*
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
36
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
37 *To be granted, apply to the Project Stics Team and then request to SIWAA*
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
38
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
39 Documentation
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
40 -------------
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
41 A tool to simulate stics rotation paralelly
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
42
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
43 Credits
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
44 -------
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
45 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
46 - Stics Site: https://www6.paca.inra.fr/stics_eng
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
47 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
48 - Copyright: INRAE
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
49 </help>
e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
siwaa
parents:
diff changeset
50 </tool>