--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preparesim.xml	Mon Sep 05 07:54:50 2022 +0000
@@ -0,0 +1,57 @@
+<tool id="CarboSeqPrepareSim" name="CarboSeqPrepareSim" version="1.0.0">
+  <description>To prepare the data for simulating</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.0.0</container>
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[
+  bash -e -c "mkdir -p data/client.files &&
+  cp ${meteo_data} data/client.files/meteo.csv &&
+  cp ${crop_data} data/client.files/crop.csv &&
+  cp ${soil_data} data/client.files/soil.csv &&
+  mkdir -p data/mapping.files &&
+  cp ${crop_mapping} data/mapping.files/crop.mapping.csv &&
+  cp ${property_mapping} data/mapping.files/property.mapping.csv &&
+  mkdir output &&
+  export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
+  cp /usr/local/src/myscripts/usercases/prepare-sim/run.r . &&
+  Rscript run.r &&
+  cp output/RothcPreparedRunnerResults.RData ${prepare_output}"
+    ]]>
+  </command>
+  <inputs>
+    <param name="meteo_data" type="data" format="csv" label="meteo data (csv file)"/>
+    <param name="crop_data" type="data" format="csv" label="crop data (csv file)"/>
+    <param name="soil_data" type="data" format="csv" label="soil data (csv file)"/>
+    <param name="crop_mapping" type="data" format="csv" label="crop mapping (csv file)"/>
+    <param name="property_mapping" type="data" format="csv" label="property mapping (csv file)"/>
+  </inputs>
+<outputs>
+  <data format='rdata' name="prepare_output" label="Rothc Prepared Runner Results"/>
+</outputs>
+<tests>
+  <test>
+    <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" />
+    <param name="crop_data" value="inputs/client.files/crop.csv" ftype="csv" />
+    <param name="soil_data" value="inputs/client.files/soil.csv" ftype="csv" />
+    <param name="crop_mapping" value="inputs/mapping.files/crop.mapping.csv" ftype="csv" />
+    <param name="property_mapping" value="inputs/mapping.files/property.mapping.csv" ftype="csv"/>
+    <output name="prepare_output">
+    <assert_contents>
+      <has_size value="5474" />
+    </assert_contents>
+    </output>
+  </test>
+</tests>
+<help>
+the CarboSeqPrepareSim tool
+===========================
+
+credits
+-------
+
+-  Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
+-  Tool Maintainer: Eric Casellas eric.casellas@inrae.fr
+-  Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
+-  Copyright: INRAE
+</help>
+</tool>