Mercurial > repos > siwaa > dairyfit_subselect

annotate subselect.xml @ 0:592df922f839 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
author siwaa
date Tue, 06 Jan 2026 15:18:16 +0000
parents
children 42116d508352
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
1 <tool id="subSelect" name="subSelect" version="1.0.0">
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
2 <description>netcdf spatial subselection</description>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
3 <requirements>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
4 <container type="singularity">docker://registry.forge.inrae.fr/dairyfit/lot1/chaine_traitement_indicateur:latest
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
5 </container>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
6 </requirements>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
7 <command detect_errors="aggressive">
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
8 <![CDATA[
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
9 mkdir -p VariableInputFolder/dummyFolder areaFolder VariableOutputFolder;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
10 cp $climateModelVariable VariableInputFolder/dummyFolder/$climateModelVariable.name;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
11 cd areaFolder;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
12 tar -xvpf $area;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
13 shpFile=\$(ls | grep shp);
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
14 cd ..;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
15 conda run --no-capture-output -n dairyfit
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
16 python /data/1_subselect_Bretagne.py
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
17 --input_dir VariableInputFolder
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
18 --shapefile areaFolder/\$shpFile
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
19 --output_dir VariableOutputFolder;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
20 cp \$(find VariableOutputFolder -type f) $climateVar
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
21 ]]>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
22 </command>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
23 <inputs>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
24 <param name="selecTag" type="text" value="" label="Selection Name"/>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
25 <param name="climateModelVariable" type="data" format="netcdf" label="Select a climate model variable file (nc file)"/>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
26 <param name="area" type="data" format="tgz" label="Select a flat archive of a area shapeFile folder (tgz file)"/>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
27 </inputs>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
28 <outputs>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
29 <data format="netcdf" name="climateVar"
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
30 label="${selecTag}${climateModelVariable.name}">
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
31 </data>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
32 </outputs>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
33 <help>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
34 Documentation
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
35 -------------
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
36 A tool to select a sub area of a netcddf file accordind to a shape file
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
37
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
38 Credits
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
39 -------
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
40 - Wrapped Tool Author:
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
41 - Site:
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
42 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
43 - Copyright: INRAE
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
44 </help>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
siwaa
parents:
diff changeset
45 </tool>