Mercurial > repos > siwaa > carboseq
comparison preparesim.xml @ 7:39eb9b8f63e6 draft
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e447822bfb34139524b626bdf1c43997acd9c28c commit e447822bfb34139524b626bdf1c43997acd9c28c-dirty"
| author | siwaa |
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| date | Mon, 05 Sep 2022 07:54:50 +0000 |
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| children |
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| 6:9382bc075d81 | 7:39eb9b8f63e6 |
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| 1 <tool id="CarboSeqPrepareSim" name="CarboSeqPrepareSim" version="1.0.0"> | |
| 2 <description>To prepare the data for simulating</description> | |
| 3 <requirements> | |
| 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.0.0</container> | |
| 5 </requirements> | |
| 6 <command detect_errors="aggressive"><![CDATA[ | |
| 7 bash -e -c "mkdir -p data/client.files && | |
| 8 cp ${meteo_data} data/client.files/meteo.csv && | |
| 9 cp ${crop_data} data/client.files/crop.csv && | |
| 10 cp ${soil_data} data/client.files/soil.csv && | |
| 11 mkdir -p data/mapping.files && | |
| 12 cp ${crop_mapping} data/mapping.files/crop.mapping.csv && | |
| 13 cp ${property_mapping} data/mapping.files/property.mapping.csv && | |
| 14 mkdir output && | |
| 15 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) && | |
| 16 cp /usr/local/src/myscripts/usercases/prepare-sim/run.r . && | |
| 17 Rscript run.r && | |
| 18 cp output/RothcPreparedRunnerResults.RData ${prepare_output}" | |
| 19 ]]> | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="meteo_data" type="data" format="csv" label="meteo data (csv file)"/> | |
| 23 <param name="crop_data" type="data" format="csv" label="crop data (csv file)"/> | |
| 24 <param name="soil_data" type="data" format="csv" label="soil data (csv file)"/> | |
| 25 <param name="crop_mapping" type="data" format="csv" label="crop mapping (csv file)"/> | |
| 26 <param name="property_mapping" type="data" format="csv" label="property mapping (csv file)"/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format='rdata' name="prepare_output" label="Rothc Prepared Runner Results"/> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" /> | |
| 34 <param name="crop_data" value="inputs/client.files/crop.csv" ftype="csv" /> | |
| 35 <param name="soil_data" value="inputs/client.files/soil.csv" ftype="csv" /> | |
| 36 <param name="crop_mapping" value="inputs/mapping.files/crop.mapping.csv" ftype="csv" /> | |
| 37 <param name="property_mapping" value="inputs/mapping.files/property.mapping.csv" ftype="csv"/> | |
| 38 <output name="prepare_output"> | |
| 39 <assert_contents> | |
| 40 <has_size value="5474" /> | |
| 41 </assert_contents> | |
| 42 </output> | |
| 43 </test> | |
| 44 </tests> | |
| 45 <help> | |
| 46 the CarboSeqPrepareSim tool | |
| 47 =========================== | |
| 48 | |
| 49 credits | |
| 50 ------- | |
| 51 | |
| 52 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr | |
| 53 - Tool Maintainer: Eric Casellas eric.casellas@inrae.fr | |
| 54 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq | |
| 55 - Copyright: INRAE | |
| 56 </help> | |
| 57 </tool> |