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comparison carboseqSimulator.xml @ 1:89c69fcbf561 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
author siwaa
date Fri, 09 Aug 2024 15:09:48 +0000
parents fb1b9308807f
children d78961e3f5ca
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0:fb1b9308807f 1:89c69fcbf561
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.1"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.9">
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-695457e0</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 bash -e -c "mkdir inputs && 7 mkdir data &&
8 mkdir output && 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) &&
12 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
13 bash -e -c "mkdir output &&
9 unzip -d input ${input} && 14 unzip -d input ${input} &&
10 set -a ;source /usr/local/src/myscripts/.env && 15 mkdir tmp &&
11 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&& 16 export TMPDIR="\${PWD}/tmp" &&
12 mv output/* ${output}" 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}"
13 ]]> 19 ]]>
14 </command> 20 </command>
15 <inputs> 21 <inputs>
16 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/> 22 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
17 </inputs> 23 </inputs>
18 <outputs> 24 <outputs>
19 <data format='rdata' name="output" label="CarboSeq output (rdata)"/> 25 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
20 </outputs> 26 </outputs>
21 <tests> 27 <tests>
28 <test>
29 <param name="input" value="input/40Sites.zip" ftype="zip" />
30 <output name="output" ftype="rdata" >
31 <assert_contents>
32 <has_size value="1156" negate="false" />
33 <has_size value="0" negate="true" />
34 </assert_contents>
35 </output>
36 </test>
22 </tests> 37 </tests>
23 <help> 38 <help>
24 the CarboSeq CarboseqSimulator tool 39 the CarboSeq CarboseqSimulator tool
25 =================================== 40 ===================================
26 41