--- a/carboseqSimulator.xml	Fri Aug 23 10:09:37 2024 +0000
+++ b/carboseqSimulator.xml	Fri Aug 23 13:19:04 2024 +0000
@@ -1,20 +1,14 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.10">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.11">
   <description>To run the CarboSeq simulator</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:74-considering-java21</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwa</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-  mkdir data &&
-  cp $__tool_directory__/ontology.owl data &&
-  cp -r $__tool_directory__/config_mappers . &&
-  cp $__tool_directory__/semantifier.jar . &&
   (env | grep DOCKER_IMAGE) &&
   printf " Image  Reg   : \$s\n" \$(env | grep DOCKER_IMAGE) &&
   bash -e -c "mkdir output &&
   unzip -d input ${input} &&
-  mkdir tmp &&
-  export TMPDIR="\${PWD}/tmp" &&
-  Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
+  Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
   cp output/* ${output}"
     ]]>
   </command>
@@ -29,7 +23,7 @@
     <param name="input" value="input/40Sites.zip" ftype="zip" />
     <output name="output" ftype="rdata" >
       	<assert_contents>
-	  <has_size value="1156" negate="false" />
+	  <has_size value="38654" negate="false" />
 	  <has_size value="0" negate="true" />
 	</assert_contents>
     </output>