--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runrothc.xml	Thu May 12 13:10:08 2022 +0000
@@ -0,0 +1,55 @@
+<tool id="CarboSeqRunRothC" name="CarboSeqRunRothC" version="1.0.0">
+  <description>To run the RothC simulator</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/record-projet-carboseq/testcaserothc:image-rothc-1.0</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+  bash -e -c "cp -r /work/csopralibs . &&
+  cp ${simulation_data} CsopraAIALInTestCase.RData &&
+  cp ${climat_data} csopralibs/data/Csopra/Climat_Csopra/CSOPRA_CLIMAT_MOIS_SAFRAN_2416.txt &&
+  cp /work/csopralibs/scripts/R/testCaseRothC.r testCaseRothC.r &&
+  sed -i 's/source(\"~\/\.Rpro/homeS <- \".\" #source(\"~\/\.Rpro/' testCaseRothC.r &&
+  sed -i 's/setwd(homeS/setwd(getwd()/' testCaseRothC.r  &&
+  sed -i 's/load(\"~\/tmp/load(\"\./' testCaseRothC.r &&
+  R -e \"source('./testCaseRothC.r', echo=TRUE)\" > ${log} &&
+  cp Rplots.pdf ${plot}"
+    ]]>
+  </command>
+  <inputs>
+    <param name="simulation_data" type="data" format="rdata" label="CarboSeq simulations data (rdata file)"/>
+    <param name="climat_data" type="data" format="txt" label="CarboSeq climat data (txt file)"/>
+  </inputs>
+<outputs>
+  <data format='txt' name="log" label="CarboSeq RothC log"/>
+  <data format='pdf' name="plot" label="CarboSeq plot"/>
+</outputs>
+<tests>
+  <test>
+    <param name="simulation_data" value="inputs/Galaxy1-CarboSeq_simulations_data.rdata" ftype="rdata" />
+    <param name="climat_data" value="inputs/CSOPRA_CLIMAT_MOIS_SAFRAN_2416.txt" ftype="txt" />
+    <output name="plot">
+    <assert_contents>
+      <has_size value="27045" delta="100" />
+    </assert_contents>
+    </output>
+    <output name="log">
+      <assert_contents>
+      <has_line line="> simTrial$runner$run()" />
+    </assert_contents>
+    </output>
+  </test>
+
+</tests>
+<help>
+the CarboSeqGetData 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>