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comparison carboseqSimulator.xml @ 7:366449cab681 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
author siwaa
date Thu, 29 Aug 2024 14:58:19 +0000
parents f9183e245cdb
children 5fdc9d0c223b
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6:f9183e245cdb 7:366449cab681
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.12"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.13">
2 <description>To run the CarboSeq simulator</description> 2 <description>To run the CarboSeq simulator</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwaa</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwaa</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
10 unzip -d input ${input} && 10 unzip -d input ${input} &&
11 cp /usr/local/src/myscripts/semantifier.jar . && 11 cp /usr/local/src/myscripts/semantifier.jar . &&
12 cp /usr/local/src/myscripts/start_server.sh . && 12 cp /usr/local/src/myscripts/start_server.sh . &&
13 cp -r /usr/local/src/myscripts/config_mappers . && 13 cp -r /usr/local/src/myscripts/config_mappers . &&
14 cp -r /usr/local/src/myscripts/data . && 14 cp -r /usr/local/src/myscripts/data . &&
15 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&& 15 Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
16 cp output/* ${output}" 16 cp output/* ${output}"
17 ]]> 17 ]]>
18 </command> 18 </command>
19 <inputs> 19 <inputs>
20 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/> 20 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>