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"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
files README.md nc2stics.xml
diffstat 2 files changed, 49 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Mon Jan 12 13:23:19 2026 +0000
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+Welcome to the folder hosting the nc2Stics tool of the dairyFit project.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nc2stics.xml	Mon Jan 12 13:23:19 2026 +0000
@@ -0,0 +1,48 @@
+<tool id="nc2Stics" name="nc2Stics" version="1.0.0">
+  <description>to convert netcdf files to climat files of Stics</description>
+  <requirements>
+    <container type="singularity">docker://registry.forge.inrae.fr/dairyfit/lot1/chaine_traitement_indicateur:latest
+    </container>
+  </requirements>
+  <command detect_errors="aggressive">
+    <![CDATA[
+	     mkdir climateInputFolder meshFolder SticsClimateOutputFolder;
+	     cd climateInputFolder;
+	     tar -xvpf $climateModelVariables;
+	     cd ../meshFolder;
+	     tar -xvpf $DRIASmesh;
+	     cd ..;
+	     conda run --no-capture-output -n dairyfit
+	     python -u /data/3_transformation_to_stics_format.py
+	     --path_model climateInputFolder
+	     --path_maille \$(find meshFolder -name *.shp)
+	     --epsg 'EPSG:27572'
+	     --output_dir SticsClimateOutputFolder
+	     --path_to_co2 $yearlyCO2;
+	     cd SticsClimateOutputFolder;
+	     tar -cvzf $SticsClimate *
+     ]]>
+  </command>
+  <inputs>
+    <param name="climateModelVariables" type="data" format="tgz" label="Select a  flat archive of a list of climate model variables (tgz file)"/>
+    <param name="DRIASmesh" type="data" format="tgz" label="Select a flat archive of a mesh shapeFile folder (tgz file)"/>    
+    <param name="yearlyCO2" type="data" format="csv" label="Select the yearly CO2 data sheet (csv)"/>
+  </inputs>
+  <outputs>
+    <data format="tgz" name="SticsClimate"
+          label="SticsClimateFiles">
+    </data>
+  </outputs>
+    <help>
+Documentation
+-------------
+A tool to convert climate netcdf files to Stics
+
+Credits
+-------
+-  Wrapped Tool Author: 
+-  Site: 
+-  Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
+-  Copyright: INRAE
+  </help>
+</tool>