--- a/preparesim.xml	Mon Sep 26 16:04:20 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<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>