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changeset 6:f9183e245cdb draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
author siwaa
date Thu, 29 Aug 2024 10:11:24 +0000
parents 3e7978af2ba2
children 366449cab681
files carboseqSimulator.xml
diffstat 1 files changed, 33 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/carboseqSimulator.xml	Wed Aug 28 14:53:30 2024 +0000
+++ b/carboseqSimulator.xml	Thu Aug 29 10:11:24 2024 +0000
@@ -1,35 +1,54 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.11">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.12">
   <description>To run the CarboSeq simulator</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwa</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwaa</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
   (env | grep DOCKER_IMAGE) &&
   printf " Image  Reg   : \$s\n" \$(env | grep DOCKER_IMAGE) &&
   bash -e -c "mkdir output &&
   unzip -d input ${input} &&
-  Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
+  cp /usr/local/src/myscripts/semantifier.jar . &&
+  cp /usr/local/src/myscripts/start_server.sh . &&
+  cp -r /usr/local/src/myscripts/config_mappers . &&
+  cp -r /usr/local/src/myscripts/data . &&
+  Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
   cp output/* ${output}"
     ]]>
   </command>
   <inputs>
     <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
+    <param name="semantifier" type="select" label="Choose the semantifier mode:">
+      <option value="modeltoolbox_sem_local" selected="true">local</option>
+      <option value="modeltoolbox_sem_remote">remote</option>
+    </param>
   </inputs>
-<outputs>
-  <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" >
+  <outputs>
+    <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input/40Sites.zip" ftype="zip" />
+      <param name="semantifier" value="modeltoolbox_sem_local" />
+      <output name="output" ftype="rdata" >
       	<assert_contents>
 	  <has_size value="38654" negate="false" />
 	  <has_size value="0" negate="true" />
 	</assert_contents>
-    </output>
-  </test>
-</tests>
-<help>
+      </output>
+    </test>
+    <test>
+      <param name="input" value="input/40Sites.zip" ftype="zip" />
+      <param name="semantifier" value="modeltoolbox_sem_remote" />
+      <output name="output" ftype="rdata" >
+      	<assert_contents>
+	  <has_size value="38654" negate="false" />
+	  <has_size value="0" negate="true" />
+	</assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help>
 the CarboSeq CarboseqSimulator tool
 ===================================