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comparison carboseqSimulator.xml @ 11:32bda6e69c5a draft default tip

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author patrick_chabrier
date Thu, 11 Jul 2024 09:40:46 +0000
parents 74a8deeedd19
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10:28139f7f1dbc 11:32bda6e69c5a
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.7"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.8">
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:develop</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 (java -Dquarkus.http.port=8282 -jar $__tool_directory__/semantifier.jar &) && 7 mkdir data &&
8 env && 8 cp $__tool_directory__/ontology.owl data &&
9 cp -r $__tool_directory__/config_mappers . &&
10 cp $__tool_directory__/semantifier.jar . &&
9 (env | grep DOCKER_IMAGE) && 11 (env | grep DOCKER_IMAGE) &&
10 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) && 12 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
11 bash -e -c "mkdir output && 13 bash -e -c "mkdir output &&
12 unzip -d input ${input} && 14 unzip -d input ${input} &&
13 mkdir tmp && 15 mkdir tmp &&
14 export TMPDIR="\${PWD}/tmp" && 16 export TMPDIR="\${PWD}/tmp" &&
15 Rscript $__tool_directory__/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&& 17 Rscript $__tool_directory__/run.r --url=https://localhost:8585/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
16 mv output/* ${output}" 18 mv output/* ${output}"
17 ]]> 19 ]]>
18 </command> 20 </command>
19 <inputs> 21 <inputs>
20 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/> 22 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>