--- a/carboseqSimulator.xml	Tue Jun 25 10:21:58 2024 +0000
+++ b/carboseqSimulator.xml	Fri Aug 09 15:09:48 2024 +0000
@@ -1,15 +1,21 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.1">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.9">
   <description>To run the CarboSeq simulator</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop-695457e0</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-  bash -e -c "mkdir inputs &&
-  mkdir output &&
+  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} &&
-  set -a ;source /usr/local/src/myscripts/.env &&
-  Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&&
-  mv output/* ${output}"
+  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}&&
+  cp output/* ${output}"
     ]]>
   </command>
   <inputs>
@@ -19,6 +25,15 @@
   <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
 </outputs>
 <tests>
+  <test>
+    <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="0" negate="true" />
+	</assert_contents>
+    </output>
+  </test>
 </tests>
 <help>
 the CarboSeq CarboseqSimulator tool