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"planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit a9c9a79dd99148422b87efce42818f7831287cdb"
author siwaa
date Wed, 11 Feb 2026 20:26:38 +0000
parents 42116d508352
children
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7cd77499d854 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit a9c9a79dd99148422b87efce42818f7831287cdb"
siwaa
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1 <tool id="subSelect" name="subSelect" version="1.0.1">
0
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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2 <description>netcdf spatial subselection</description>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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3 <requirements>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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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"
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5 </container>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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6 </requirements>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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7 <command detect_errors="aggressive">
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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8 <![CDATA[
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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9 mkdir -p VariableInputFolder/dummyFolder areaFolder VariableOutputFolder;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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10 cp $climateModelVariable VariableInputFolder/dummyFolder/$climateModelVariable.name;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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11 cd areaFolder;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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12 tar -xvpf $area;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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13 shpFile=\$(ls | grep shp);
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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14 cd ..;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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15 conda run --no-capture-output -n dairyfit
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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16 python /data/1_subselect_Bretagne.py
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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17 --input_dir VariableInputFolder
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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18 --shapefile areaFolder/\$shpFile
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7cd77499d854 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit a9c9a79dd99148422b87efce42818f7831287cdb"
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19 --counties "$counties"
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592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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20 --output_dir VariableOutputFolder;
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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21 cp \$(find VariableOutputFolder -type f) $climateVar
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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22 ]]>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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23 </command>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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24 <inputs>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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25 <param name="selecTag" type="text" value="" label="Selection Name"/>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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26 <param name="climateModelVariable" type="data" format="netcdf" label="Select a climate model variable file (nc file)"/>
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7cd77499d854 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit a9c9a79dd99148422b87efce42818f7831287cdb"
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27 <param name="area" type="data" format="tgz" label="Select a flat archive of a area shapeFile folder (tgz file)"/>
7cd77499d854 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit a9c9a79dd99148422b87efce42818f7831287cdb"
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28 <param name="counties" type="text" value="Côtes-d'Armor Finistère Ille-et-Vilaine Morbihan Loire-Atlantique Mayenne Sarthe Manche" label="List of counties" sanitize="False"/>
0
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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29 </inputs>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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30 <outputs>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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31 <data format="netcdf" name="climateVar"
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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32 label="${selecTag}${climateModelVariable.name}">
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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33 </data>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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34 </outputs>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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35 <help>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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36 Documentation
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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37 -------------
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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38 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"
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39
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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40 Credits
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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41 -------
1
42116d508352 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 94e6cf80413085adde18ed28df9261be321c189f"
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42 - Wrapped Tool Author: Renan Le Roux renan.le-roux@inrae.fr
42116d508352 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 94e6cf80413085adde18ed28df9261be321c189f"
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43 - Site: https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox
0
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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44 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
1
42116d508352 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit 94e6cf80413085adde18ed28df9261be321c189f"
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45 - tool Site : https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox
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46 - Copyright: INRAE
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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47 </help>
592df922f839 "planemo upload for repository https://forge.inrae.fr/dairyfit/lot2/dairyfit-toolbox commit bd901a6094132b68fec857f15f1f7f8345687250"
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48 </tool>