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comparison carboseqSimulator.xml @ 6:f9183e245cdb draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
author siwaa
date Thu, 29 Aug 2024 10:11:24 +0000
parents a069fc43b0b1
children 366449cab681
comparison
equal deleted inserted replaced
5:3e7978af2ba2 6:f9183e245cdb
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.11"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.12">
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:siwa</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[
7 (env | grep DOCKER_IMAGE) && 7 (env | grep DOCKER_IMAGE) &&
8 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) && 8 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
9 bash -e -c "mkdir output && 9 bash -e -c "mkdir output &&
10 unzip -d input ${input} && 10 unzip -d input ${input} &&
11 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --NBCores=\${GALAXY_SLOTS:-4}&& 11 cp /usr/local/src/myscripts/semantifier.jar . &&
12 cp /usr/local/src/myscripts/start_server.sh . &&
13 cp -r /usr/local/src/myscripts/config_mappers . &&
14 cp -r /usr/local/src/myscripts/data . &&
15 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
12 cp output/* ${output}" 16 cp output/* ${output}"
13 ]]> 17 ]]>
14 </command> 18 </command>
15 <inputs> 19 <inputs>
16 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/> 20 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
21 <param name="semantifier" type="select" label="Choose the semantifier mode:">
22 <option value="modeltoolbox_sem_local" selected="true">local</option>
23 <option value="modeltoolbox_sem_remote">remote</option>
24 </param>
17 </inputs> 25 </inputs>
18 <outputs> 26 <outputs>
19 <data format='rdata' name="output" label="CarboSeq output (rdata)"/> 27 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
20 </outputs> 28 </outputs>
21 <tests> 29 <tests>
22 <test> 30 <test>
23 <param name="input" value="input/40Sites.zip" ftype="zip" /> 31 <param name="input" value="input/40Sites.zip" ftype="zip" />
24 <output name="output" ftype="rdata" > 32 <param name="semantifier" value="modeltoolbox_sem_local" />
33 <output name="output" ftype="rdata" >
25 <assert_contents> 34 <assert_contents>
26 <has_size value="38654" negate="false" /> 35 <has_size value="38654" negate="false" />
27 <has_size value="0" negate="true" /> 36 <has_size value="0" negate="true" />
28 </assert_contents> 37 </assert_contents>
29 </output> 38 </output>
30 </test> 39 </test>
31 </tests> 40 <test>
32 <help> 41 <param name="input" value="input/40Sites.zip" ftype="zip" />
42 <param name="semantifier" value="modeltoolbox_sem_remote" />
43 <output name="output" ftype="rdata" >
44 <assert_contents>
45 <has_size value="38654" negate="false" />
46 <has_size value="0" negate="true" />
47 </assert_contents>
48 </output>
49 </test>
50 </tests>
51 <help>
33 the CarboSeq CarboseqSimulator tool 52 the CarboSeq CarboseqSimulator tool
34 =================================== 53 ===================================
35 54
36 credits 55 credits
37 ------- 56 -------