# HG changeset patch
# User siwaa
# Date 1734596455 0
# Node ID 56b0bf51585a08383333e3b503774d7a8d2a5f9a
# Parent  5ed871d666b4a59d39789a5941a7d887368f59fd
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/806f38d2aa86cb93ec97c29004b0b8cc5bc28033/toos/CarboSeqSimulator commit 806f38d2aa86cb93ec97c29004b0b8cc5bc28033-dirty"

diff -r 5ed871d666b4 -r 56b0bf51585a carboseqSimulator.xml
--- a/carboseqSimulator.xml	Thu Dec 12 14:38:52 2024 +0000
+++ b/carboseqSimulator.xml	Thu Dec 19 08:20:55 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.18">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.19">
   <description>To run the CarboSeq simulator</description>
   <requirements>
     <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container>
@@ -17,6 +17,7 @@
   cp -r /usr/local/src/myscripts/config_mappers . &&
   cp -r /usr/local/src/myscripts/data . &&
   cp /usr/local/src/myscripts/scenarios/run-sim-perf/run.r . &&
+  set -a && . /usr/local/src/myscripts/.env && set +a &&
   Rscript ./run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
   cp output/* ${output}"
     ]]>
@@ -33,21 +34,21 @@
   </outputs>
   <tests>
     <test>
-      <param name="input" value="input/40Sites.zip" ftype="zip" />
+      <param name="input" value="input/inputFiles.zip" ftype="zip" />
       <param name="semantifier" value="modeltoolbox_sem_local" />
       <output name="output" ftype="rdata" >
       	<assert_contents>
-	  <has_size value="1334" negate="false" />
+	  <has_size value="595" negate="false" />
 	  <has_size value="0" negate="true" />
 	</assert_contents>
       </output>
     </test>
     <test>
-      <param name="input" value="input/40Sites.zip" ftype="zip" />
+      <param name="input" value="input/inputFiles.zip" ftype="zip" />
       <param name="semantifier" value="modeltoolbox_sem_remote" />
       <output name="output" ftype="rdata" >
       	<assert_contents>
-	  <has_size value="1334" negate="false" />
+	  <has_size value="595" negate="false" />
 	  <has_size value="0" negate="true" />
 	</assert_contents>
       </output>
diff -r 5ed871d666b4 -r 56b0bf51585a test-data/input/inputFiles.zip
Binary file test-data/input/inputFiles.zip has changed