Mercurial > repos > siwaa > sms

annotate SMSticsTool-9.2.xml @ 0:ab62b4ecd5b9 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 5e434da355bade7d12364ccbd84b53848e6fa4c5"
author siwaa
date Mon, 18 Jul 2022 10:54:39 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
1 <tool id="SMSticsTool-9.2" name="sms_stics-9.2" version="1.0.0">
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
2 <description>to run the Stics simulator on the SMS DB [Stics-9.2]</description>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
3 <requirements>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
4 <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_sms:9.2</container>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
5 </requirements>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
6 <command detect_errors="aggressive">
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
7 <![CDATA[
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
8 cp -r /home/rstudio/JavaSTICS-1.41-stics-9.2/ . &&
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
9 cp -R /home/rstudio/EvaluationReports . &&
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
10 unzip ${SMSdb} &&
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
11 cp ${plan} USMlist.csv &&
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
12 Rscript --verbose $__tool_directory__/eval_only_stics_on_sms.R &&
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
13 zip -r eval.zip work/eval_* &&
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
14 cp eval.zip ${evalFolder}
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
15 ]]>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
16 </command>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
17 <inputs>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
18 <param name="SMSdb" type="data" format="zip" label="Select a stics SMS DB (zip file)"/>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
19 <param name="plan" type="data" format="csv" label="Select a plan (csv file)"/>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
20 </inputs>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
21 <outputs>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
22 <data format="zip" name="evalFolder"
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
23 label="Stics SMS Evaluation Folder">
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
24 </data>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
25 </outputs>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
26 <tests>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
27 </tests>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
28 <help>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
29 *The usage of this tool is restricted to the user of the stics_authorized group.*
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
30
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
31 *To be granted, apply to the Project Stics Team and then request to SIWAA*
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
32
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
33 Documentation
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
34 -------------
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
35 A tool to run the Stics simulator on a Stics SMS database.
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
36
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
37 Credits
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
38 -------
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
39 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
40 - Stics Site: https://www6.paca.inra.fr/stics_eng
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
41 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
42 - Copyright: INRAE
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
43 </help>
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
siwaa
parents:
diff changeset
44 </tool>