Mercurial > repos > siwaa > dairyfit_nctostics

annotate nc2stics.xml @ 0:93879a20d221 draft default tip

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 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
author siwaa
date Mon, 12 Jan 2026 13:23:19 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
1 <tool id="nc2Stics" name="nc2Stics" version="1.0.0">
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
2 <description>to convert netcdf files to climat files of Stics</description>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
3 <requirements>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
4 <container type="singularity">docker://registry.forge.inrae.fr/dairyfit/lot1/chaine_traitement_indicateur:latest
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
5 </container>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
6 </requirements>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
7 <command detect_errors="aggressive">
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
8 <![CDATA[
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
9 mkdir climateInputFolder meshFolder SticsClimateOutputFolder;
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
10 cd climateInputFolder;
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
11 tar -xvpf $climateModelVariables;
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
12 cd ../meshFolder;
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
13 tar -xvpf $DRIASmesh;
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
14 cd ..;
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
15 conda run --no-capture-output -n dairyfit
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
16 python -u /data/3_transformation_to_stics_format.py
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
17 --path_model climateInputFolder
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
18 --path_maille \$(find meshFolder -name *.shp)
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
19 --epsg 'EPSG:27572'
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
20 --output_dir SticsClimateOutputFolder
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
21 --path_to_co2 $yearlyCO2;
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
22 cd SticsClimateOutputFolder;
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
23 tar -cvzf $SticsClimate *
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
24 ]]>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
25 </command>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
26 <inputs>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
27 <param name="climateModelVariables" type="data" format="tgz" label="Select a flat archive of a list of climate model variables (tgz file)"/>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
28 <param name="DRIASmesh" type="data" format="tgz" label="Select a flat archive of a mesh shapeFile folder (tgz file)"/>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
29 <param name="yearlyCO2" type="data" format="csv" label="Select the yearly CO2 data sheet (csv)"/>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
30 </inputs>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
31 <outputs>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
32 <data format="tgz" name="SticsClimate"
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
33 label="SticsClimateFiles">
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
34 </data>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
35 </outputs>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
36 <help>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
37 Documentation
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
38 -------------
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
39 A tool to convert climate netcdf files to Stics
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
40
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
41 Credits
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
42 -------
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
43 - Wrapped Tool Author:
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
44 - Site:
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
45 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
46 - Copyright: INRAE
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
47 </help>
93879a20d221 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 065e7bbcfbc2bdaede2382f967f1a13a2e08e184"
siwaa
parents:
diff changeset
48 </tool>