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comparison carboseqSimulator.xml @ 0:df440714e49a draft

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author patrick_chabrier
date Tue, 04 Jun 2024 18:13:35 +0000
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1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.0">
2 <description>To run the CarboSeq simulator</description>
3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/csopralibs_dev:paralleltoparallelly</container>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 bash -e -c "mkdir inputs &&
8 unzip -d input ${input} &&
9 set -a ;source /usr/local/src/myscripts/.env &&
10 export CARBOSEQPREPROCESSOR_INPUT_DIR=\$(realpath -s input)
11 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
12 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r &&
13 cd output &&
14 zip -r output.zip * &&
15 cp output.zip ${output}"
16 ]]>
17 </command>
18 <inputs>
19 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
20 </inputs>
21 <outputs>
22 <data format='zip' name="output" label="CarboSeq output (zip)"/>
23 </outputs>
24 <tests>
25 </tests>
26 <help>
27 the CarboSeq CarboseqSimulator tool
28 ===================================
29
30 credits
31 -------
32 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
33 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
34 - Copyright: INRAE
35 </help>
36 </tool>