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comparison carboseqSimulator.xml @ 4:a069fc43b0b1 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty"
author siwaa
date Fri, 23 Aug 2024 13:19:04 +0000
parents d753f3430970
children f9183e245cdb
comparison
equal deleted inserted replaced
3:d753f3430970 4:a069fc43b0b1
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.10"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.11">
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:74-considering-java21</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwa</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 mkdir data &&
8 cp $__tool_directory__/ontology.owl data &&
9 cp -r $__tool_directory__/config_mappers . &&
10 cp $__tool_directory__/semantifier.jar . &&
11 (env | grep DOCKER_IMAGE) && 7 (env | grep DOCKER_IMAGE) &&
12 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) && 8 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
13 bash -e -c "mkdir output && 9 bash -e -c "mkdir output &&
14 unzip -d input ${input} && 10 unzip -d input ${input} &&
15 mkdir tmp && 11 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
16 export TMPDIR="\${PWD}/tmp" &&
17 Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&&
18 cp output/* ${output}" 12 cp output/* ${output}"
19 ]]> 13 ]]>
20 </command> 14 </command>
21 <inputs> 15 <inputs>
22 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/> 16 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
27 <tests> 21 <tests>
28 <test> 22 <test>
29 <param name="input" value="input/40Sites.zip" ftype="zip" /> 23 <param name="input" value="input/40Sites.zip" ftype="zip" />
30 <output name="output" ftype="rdata" > 24 <output name="output" ftype="rdata" >
31 <assert_contents> 25 <assert_contents>
32 <has_size value="1156" negate="false" /> 26 <has_size value="38654" negate="false" />
33 <has_size value="0" negate="true" /> 27 <has_size value="0" negate="true" />
34 </assert_contents> 28 </assert_contents>
35 </output> 29 </output>
36 </test> 30 </test>
37 </tests> 31 </tests>