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comparison carboseqSimulator.xml @ 16:5ed871d666b4 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/be8c2ab794a3722ee6edc3c9f7e73ccc45806f31/toos/CarboSeqSimulator commit be8c2ab794a3722ee6edc3c9f7e73ccc45806f31-dirty"
author siwaa
date Thu, 12 Dec 2024 14:38:52 +0000
parents de71663fbce4
children 56b0bf51585a
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15:de71663fbce4 16:5ed871d666b4
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.17"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.18">
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:main</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
14 unzip -d input ${input} && 14 unzip -d input ${input} &&
15 cp /usr/local/src/myscripts/semantifier.jar . && 15 cp /usr/local/src/myscripts/semantifier.jar . &&
16 cp /usr/local/src/myscripts/start_server.sh . && 16 cp /usr/local/src/myscripts/start_server.sh . &&
17 cp -r /usr/local/src/myscripts/config_mappers . && 17 cp -r /usr/local/src/myscripts/config_mappers . &&
18 cp -r /usr/local/src/myscripts/data . && 18 cp -r /usr/local/src/myscripts/data . &&
19 Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&& 19 cp /usr/local/src/myscripts/scenarios/run-sim-perf/run.r . &&
20 Rscript ./run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
20 cp output/* ${output}" 21 cp output/* ${output}"
21 ]]> 22 ]]>
22 </command> 23 </command>
23 <inputs> 24 <inputs>
24 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/> 25 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>