--- a/carboseqSimulator.xml	Thu Jul 11 09:39:17 2024 +0000
+++ b/carboseqSimulator.xml	Thu Jul 11 09:40:46 2024 +0000
@@ -1,18 +1,20 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.7">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.8">
   <description>To run the CarboSeq simulator</description>
   <requirements>
     <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-  (java -Dquarkus.http.port=8282 -jar  $__tool_directory__/semantifier.jar &) &&
-  env &&
+  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 --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&&
+  Rscript $__tool_directory__/run.r --url=https://localhost:8585/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
   mv output/* ${output}"
     ]]>
   </command>