Mercurial > repos > patrick_chabrier > carboseq_s

changeset 0:df440714e49a draft

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Uploaded
author patrick_chabrier
date Tue, 04 Jun 2024 18:13:35 +0000
parents
children 8e2dd4aec727
files carboseqSimulator.xml
diffstat 1 files changed, 36 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carboseqSimulator.xml	Tue Jun 04 18:13:35 2024 +0000
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+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.0">
+  <description>To run the CarboSeq simulator</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/csopralibs_dev:paralleltoparallelly</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+  bash -e -c "mkdir inputs &&
+  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}"
+    ]]>
+  </command>
+  <inputs>
+    <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
+  </inputs>
+<outputs>
+  <data format='zip' name="output" label="CarboSeq output (zip)"/>
+</outputs>
+<tests>
+</tests>
+<help>
+the CarboSeq CarboseqSimulator tool
+===================================
+
+credits
+-------
+-  Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
+-  Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
+-  Copyright: INRAE
+</help>
+</tool>