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comparison runsim.xml @ 8:eff04f7eec9f draft

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"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 39eb9b8f63e6
children f60bb19f7880
comparison
equal deleted inserted replaced
7:39eb9b8f63e6 8:eff04f7eec9f
1 <tool id="CarboSeqRunSim" name="CarboSeqRunSim" version="1.0.0"> 1 <tool id="CarboSeqRunSim" name="CarboSeqRunSim" version="1.1.0">
2 <description>To run the simulator</description> 2 <description>To run the simulator</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.0.0</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.1.0</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 bash -e -c "mkdir -p data/client.files && 7 bash -e -c "mkdir inputs &&
8 cp ${meteo_data} data/client.files/meteo.csv && 8 cp ${meteo_data} inputs/meteo.csv &&
9 cp ${crop_data} data/client.files/crop.csv && 9 cp ${crop_data} inputs/crop.csv &&
10 cp ${soil_data} data/client.files/soil.csv && 10 cp ${soil_data} inputs/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 && 11 mkdir output &&
15 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) && 12 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
16 cp /usr/local/src/myscripts/usercases/run-sim/run.r . && 13 export CSVMAPPER_INPUT_DIR=\$(realpath -s inputs) &&
17 Rscript run.r && 14 #if $id_pairs
15 export CSOPRALIBS_ID_IDSUCC_CSV_FILE=${id_pairs} &&
16 #end if
17 export CSOPRALIBS_SIM_PARAMS_IMPLEMENTATION=${simulator} &&
18 Rscript /usr/local/src/myscripts/usercases/run-sim/run.r &&
18 cp output/SimulationSOCResults.RData ${run_output}" 19 cp output/SimulationSOCResults.RData ${run_output}"
19 ]]> 20 ]]>
20 </command> 21 </command>
21 <inputs> 22 <inputs>
22 <param name="meteo_data" type="data" format="csv" label="meteo data (csv file)"/> 23 <param name="simulator" type="select" label="Simulator">
23 <param name="crop_data" type="data" format="csv" label="crop data (csv file)"/> 24 <option value="rothC" selected="true">rothC</option>
24 <param name="soil_data" type="data" format="csv" label="soil data (csv file)"/> 25 <option value="soilr">soilr</option>
25 <param name="crop_mapping" type="data" format="csv" label="crop mapping (csv file)"/> 26 </param>
26 <param name="property_mapping" type="data" format="csv" label="property mapping (csv file)"/> 27 <param name="meteo_data" type="data" format="csv" label="Meteo data (csv file)"/>
28 <param name="crop_data" type="data" format="csv" label="Crop data (csv file)"/>
29 <param name="soil_data" type="data" format="csv" label="Soil data (csv file)"/>
30 <param name="id_pairs" type="data" optional="true" format="csv" label="Id pairs (csv file)"/>
27 </inputs> 31 </inputs>
28 <outputs> 32 <outputs>
29 <data format='rdata' name="run_output" label="Simulation SOC Results"/> 33 <data format='rdata' name="run_output" label="Simulation SOC Results"/>
30 </outputs> 34 </outputs>
31 <tests> 35 <tests>
32 <test> 36 <test>
37 <param name="simulator" value="rothC" />
38 <param name="id_pairs" value="outputs/id-idSucc-pairs.csv" ftype="csv"/>
33 <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" /> 39 <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" /> 40 <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" /> 41 <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="run_output"> 42 <output name="run_output">
39 <assert_contents> 43 <assert_contents>
40 <has_size value="5462" delta="100" /> 44 <has_size value="5462" delta="100" />
41 </assert_contents> 45 </assert_contents>
42 </output> 46 </output>
43 </test> 47 </test>
44 </tests> 48 </tests>
45 <help> 49 <help>
46 the CarboSeqPrepareSim tool 50 the CarboSeq run-sim tool
47 =========================== 51 ==========================
48 52
49 credits 53 credits
50 ------- 54 -------
51 55
52 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr 56 - 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 57 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
55 - Copyright: INRAE 58 - Copyright: INRAE
56 </help> 59 </help>
57 </tool> 60 </tool>