Mercurial > repos > patrick_chabrier > carboseq_s

changeset 1:8e2dd4aec727 draft

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Uploaded
author siwaa
date Tue, 25 Jun 2024 10:36:43 +0000
parents df440714e49a
children bf6c51b72a10
files carboseqSimulator.xml
diffstat 1 files changed, 6 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/carboseqSimulator.xml	Tue Jun 04 18:13:35 2024 +0000
+++ b/carboseqSimulator.xml	Tue Jun 25 10:36:43 2024 +0000
@@ -1,25 +1,22 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.0">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.1">
   <description>To run the CarboSeq simulator</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/csopralibs_dev:paralleltoparallelly</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop-695457e0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
   bash -e -c "mkdir inputs &&
+  mkdir output &&
   unzip -d input ${input} &&
   set -a ;source /usr/local/src/myscripts/.env &&
-  export CARBOSEQPREPROCESSOR_INPUT_DIR=\$(realpath -s input)
-  export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
-  Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r &&
-  cd output &&
-  zip -r output.zip * &&
-  cp output.zip ${output}"
+  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}"
     ]]>
   </command>
   <inputs>
     <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
   </inputs>
 <outputs>
-  <data format='zip' name="output" label="CarboSeq output (zip)"/>
+  <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
 </outputs>
 <tests>
 </tests>