--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/subselect.xml	Tue Jan 06 15:18:16 2026 +0000
@@ -0,0 +1,45 @@
+<tool id="subSelect" name="subSelect" version="1.0.0">
+  <description>netcdf spatial subselection</description>
+  <requirements>
+    <container type="singularity">docker://registry.forge.inrae.fr/dairyfit/lot1/chaine_traitement_indicateur:latest
+    </container>
+  </requirements>
+  <command detect_errors="aggressive">
+    <![CDATA[
+	     mkdir -p VariableInputFolder/dummyFolder areaFolder VariableOutputFolder;
+	     cp $climateModelVariable VariableInputFolder/dummyFolder/$climateModelVariable.name;
+	     cd areaFolder;
+	     tar -xvpf $area;
+	     shpFile=\$(ls | grep shp);
+	     cd ..;
+	     conda run --no-capture-output -n dairyfit
+	     python /data/1_subselect_Bretagne.py
+             --input_dir VariableInputFolder
+             --shapefile areaFolder/\$shpFile
+             --output_dir VariableOutputFolder;
+	     cp \$(find VariableOutputFolder -type f) $climateVar
+     ]]>
+  </command>
+  <inputs>
+    <param name="selecTag" type="text" value="" label="Selection Name"/>
+    <param name="climateModelVariable" type="data" format="netcdf" label="Select a climate model variable file (nc file)"/>
+    <param name="area" type="data" format="tgz" label="Select a flat archive of a area shapeFile folder (tgz file)"/>    
+  </inputs>
+  <outputs>
+    <data format="netcdf" name="climateVar"
+          label="${selecTag}${climateModelVariable.name}">
+    </data>
+  </outputs>
+    <help>
+Documentation
+-------------
+A tool to select a sub area of a netcddf file accordind to a shape file
+
+Credits
+-------
+-  Wrapped Tool Author: 
+-  Site: 
+-  Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
+-  Copyright: INRAE
+  </help>
+</tool>