Mercurial > repos > siwaa > carboseq
comparison findidpairs.xml @ 8:eff04f7eec9f draft
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
| author | siwaa |
|---|---|
| date | Mon, 26 Sep 2022 15:54:42 +0000 |
| parents | |
| children | b75e5e1a0646 |
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| 7:39eb9b8f63e6 | 8:eff04f7eec9f |
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| 1 <tool id="CarboSeqFindIdPairs" name="CarboSeqFindIdPairs" version="1.0.0"> | |
| 2 <description>To get IdPairs</description> | |
| 3 <requirements> | |
| 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.1.0</container> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 bash -e -c "mkdir inputs && | |
| 8 cp ${meteo_data} inputs/meteo.csv && | |
| 9 cp ${crop_data} inputs/crop.csv && | |
| 10 cp ${soil_data} inputs/soil.csv && | |
| 11 mkdir output && | |
| 12 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) && | |
| 13 export CSVMAPPER_INPUT_DIR=\$(realpath -s inputs) && | |
| 14 Rscript /usr/local/src/myscripts/usercases/find-idPairs/run.r && | |
| 15 cp output/id-idSucc-pairs.csv ${findpairs_output}" | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param name="meteo_data" type="data" format="csv" label="Meteo data (csv file)"/> | |
| 20 <param name="crop_data" type="data" format="csv" label="Crop data (csv file)"/> | |
| 21 <param name="soil_data" type="data" format="csv" label="Soil data (csv file)"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format='csv' name="findpairs_output" label="IdPairs"/> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" /> | |
| 29 <param name="crop_data" value="inputs/client.files/crop.csv" ftype="csv" /> | |
| 30 <param name="soil_data" value="inputs/client.files/soil.csv" ftype="csv" /> | |
| 31 <output name="findpairs_output" file="outputs/id-idSucc-pairs.csv" /> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help> | |
| 35 the CarboSeq find-idpairs tool | |
| 36 ============================== | |
| 37 | |
| 38 credits | |
| 39 ------- | |
| 40 | |
| 41 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr | |
| 42 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq | |
| 43 - Copyright: INRAE | |
| 44 </help> | |
| 45 </tool> |