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comparison subselect.xml @ 0:592df922f839 draft

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"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
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1 <tool id="subSelect" name="subSelect" version="1.0.0">
2 <description>netcdf spatial subselection</description>
3 <requirements>
4 <container type="singularity">docker://registry.forge.inrae.fr/dairyfit/lot1/chaine_traitement_indicateur:latest
5 </container>
6 </requirements>
7 <command detect_errors="aggressive">
8 <![CDATA[
9 mkdir -p VariableInputFolder/dummyFolder areaFolder VariableOutputFolder;
10 cp $climateModelVariable VariableInputFolder/dummyFolder/$climateModelVariable.name;
11 cd areaFolder;
12 tar -xvpf $area;
13 shpFile=\$(ls | grep shp);
14 cd ..;
15 conda run --no-capture-output -n dairyfit
16 python /data/1_subselect_Bretagne.py
17 --input_dir VariableInputFolder
18 --shapefile areaFolder/\$shpFile
19 --output_dir VariableOutputFolder;
20 cp \$(find VariableOutputFolder -type f) $climateVar
21 ]]>
22 </command>
23 <inputs>
24 <param name="selecTag" type="text" value="" label="Selection Name"/>
25 <param name="climateModelVariable" type="data" format="netcdf" label="Select a climate model variable file (nc file)"/>
26 <param name="area" type="data" format="tgz" label="Select a flat archive of a area shapeFile folder (tgz file)"/>
27 </inputs>
28 <outputs>
29 <data format="netcdf" name="climateVar"
30 label="${selecTag}${climateModelVariable.name}">
31 </data>
32 </outputs>
33 <help>
34 Documentation
35 -------------
36 A tool to select a sub area of a netcddf file accordind to a shape file
37
38 Credits
39 -------
40 - Wrapped Tool Author:
41 - Site:
42 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
43 - Copyright: INRAE
44 </help>
45 </tool>