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comparison carboseqSimulator.xml @ 17:56b0bf51585a draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/806f38d2aa86cb93ec97c29004b0b8cc5bc28033/toos/CarboSeqSimulator commit 806f38d2aa86cb93ec97c29004b0b8cc5bc28033-dirty"
author siwaa
date Thu, 19 Dec 2024 08:20:55 +0000
parents 5ed871d666b4
children ce2b35fc669b
comparison
equal deleted inserted replaced
16:5ed871d666b4 17:56b0bf51585a
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.18"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.19">
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[
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 cp /usr/local/src/myscripts/scenarios/run-sim-perf/run.r . && 19 cp /usr/local/src/myscripts/scenarios/run-sim-perf/run.r . &&
20 set -a && . /usr/local/src/myscripts/.env && set +a &&
20 Rscript ./run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&& 21 Rscript ./run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
21 cp output/* ${output}" 22 cp output/* ${output}"
22 ]]> 23 ]]>
23 </command> 24 </command>
24 <inputs> 25 <inputs>
31 <outputs> 32 <outputs>
32 <data format='rdata' name="output" label="CarboSeq output (rdata)"/> 33 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
33 </outputs> 34 </outputs>
34 <tests> 35 <tests>
35 <test> 36 <test>
36 <param name="input" value="input/40Sites.zip" ftype="zip" /> 37 <param name="input" value="input/inputFiles.zip" ftype="zip" />
37 <param name="semantifier" value="modeltoolbox_sem_local" /> 38 <param name="semantifier" value="modeltoolbox_sem_local" />
38 <output name="output" ftype="rdata" > 39 <output name="output" ftype="rdata" >
39 <assert_contents> 40 <assert_contents>
40 <has_size value="1334" negate="false" /> 41 <has_size value="595" negate="false" />
41 <has_size value="0" negate="true" /> 42 <has_size value="0" negate="true" />
42 </assert_contents> 43 </assert_contents>
43 </output> 44 </output>
44 </test> 45 </test>
45 <test> 46 <test>
46 <param name="input" value="input/40Sites.zip" ftype="zip" /> 47 <param name="input" value="input/inputFiles.zip" ftype="zip" />
47 <param name="semantifier" value="modeltoolbox_sem_remote" /> 48 <param name="semantifier" value="modeltoolbox_sem_remote" />
48 <output name="output" ftype="rdata" > 49 <output name="output" ftype="rdata" >
49 <assert_contents> 50 <assert_contents>
50 <has_size value="1334" negate="false" /> 51 <has_size value="595" negate="false" />
51 <has_size value="0" negate="true" /> 52 <has_size value="0" negate="true" />
52 </assert_contents> 53 </assert_contents>
53 </output> 54 </output>
54 </test> 55 </test>
55 </tests> 56 </tests>