Mercurial > repos > siwaa > azodyn
changeset 5:49c988e63e6b draft
"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/3a14800d8c700f5acdf49d564adc9fe820aa1c25 commit 3a14800d8c700f5acdf49d564adc9fe820aa1c25-dirty"
| author | siwaa |
|---|---|
| date | Thu, 25 Aug 2022 10:47:57 +0000 |
| parents | 5deede146fb6 |
| children | a33145af2dbd |
| files | test-data/inputs/AzodynPea_input.csv test-data/inputs/AzodynPea_meteo.zip test-data/inputs/AzodynPea_output.csv tool_AZODYN.xml tool_AZODYN.xml.bak tool_defaults_AZODYN.xml |
| diffstat | 6 files changed, 74 insertions(+), 60 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/AzodynPea_input.csv Thu Aug 25 10:47:57 2022 +0000 @@ -0,0 +1,5 @@ +cPlant.coef_tot_a;condClimate.meteo_file +1.25;meteo1.csv +1.5;meteo1.csv +1.0;meteo2.csv +1.25;meteo2.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/AzodynPea_output.csv Thu Aug 25 10:47:57 2022 +0000 @@ -0,0 +1,3 @@ +id;path;integration +LAI;view/AzodynPea:PlantGrowthPea.LAI;all +MS;view/AzodynPea:PlantGrowthPea.MS;all
--- a/tool_AZODYN.xml Tue May 03 10:17:50 2022 +0000 +++ b/tool_AZODYN.xml Thu Aug 25 10:47:57 2022 +0000 @@ -24,6 +24,26 @@ <outputs> <data format="zip" name="simresults" /> </outputs> + <tests> + <test> + <param name="crop_type" value="AzodynPea.vpz" /> + <param name="input_meteo" value="inputs/AzodynPea_meteo.zip" ftype="zip" /> + <param name="file_input" value="inputs/AzodynPea_input.csv" ftype="csv" /> + <param name="file_outputs" value="inputs/AzodynPea_output.csv" ftype="csv" /> + <output name="simresults"> + <assert_contents> + <has_archive_member path="simresults_LAI.txt"> + <has_text text="0;0;0;0" /> + <has_text text="0.02230323" /> + </has_archive_member> + <has_archive_member path="simresults_MS.txt"> + <has_text text="0;0;0;0" /> + <has_text text="1.568" /> + </has_archive_member> + </assert_contents> + </output> + </test> +</tests> <help><![CDATA[ AZODYN crop models simulations ==============================
--- a/tool_AZODYN.xml.bak Tue May 03 10:17:50 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -<tool id="AZODYN" name="AZODYN crop models simulations" version="1.0.0"> - <description></description> - <requirements> - <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:ub2004_vle21</container> - </requirements> - <command detect_errors="aggressive"> - unzip ${input_meteo}; - dos2unix -n ${file_input} internal_inputAZODYN.csv; - dos2unix -n ${file_outputs} internal_outputAZODYN.csv; - /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R ${crop_type} AZODYN internal_inputAZODYN.csv internal_outputAZODYN.csv \${GALAXY_SLOTS:-2}"; - zip temp_results.zip simresults_*.txt; - cp temp_results.zip ${simresults}; - </command> - <inputs> - <param name="crop_type" type="select" label="Select crop to simulate"> - <option value="AzodynPea.vpz">Pea</option> - <option value="AzodynWheat.vpz">Wheat</option> - <option value="AzodynBarley.vpz">Barley</option> - </param> - <param name="input_meteo" type="data" format="zip" label="Wheater serie input files (zip file)"/> - <param name="file_input" type="data" format="csv" label="Crop model input values"/> - <param name="file_outputs" type="data" format="csv" label="Outputs to simulate"/> - </inputs> - <outputs> - <data format="zip" name="simresults" /> - </outputs> - <help><![CDATA[ -AZODYN crop models simulations -============================== - -Inputs: -------- - -- Zip file of wheather series -- Input values of the crop model (1 simulation per row) -- Identification of the crop model output to simulate. - -Outputs: --------- - -- Zip file of the crop model simulation values (1 file per output) - -Example: --------- - -- Select 'Pea' as the crop model to use -- Copy to your history files 'AzodynPea_meteo.zip', 'AzodynPea_input.csv' and 'AzodynPea_output.csv' from the AZODYN shared dataset. -- Fill file names and choose the adequate number of cores. -- And then execute - -Credits: --------- - -- Author: Ronan Trépos ronan.trepos@inrae.fr -- Wrapper Maintainer: Ronan Trépos ronan.trepos@inrae.fr -- Tool Maintainer: Ronan Trépos ronan.trepos@inrae.fr -- Copyright: INRAE]]> - </help> -</tool> -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_defaults_AZODYN.xml Thu Aug 25 10:47:57 2022 +0000 @@ -0,0 +1,46 @@ +<tool id="AZODYNdefaults" name="AZODYN crop models default inputs and outputs" version="1.0.0"> + <description></description> + <requirements> + <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:ub2004_vle21</container> + </requirements> + <command detect_errors="aggressive"> + /bin/bash -c "Rscript --verbose /data/rDefaultAzodynSunflo.R ${crop_type} AZODYN"; + cp file_default_input.csv ${inputs}; + cp file_default_output.csv ${outputs}; + </command> + <inputs> + <param name="crop_type" type="select" label="Select crop"> + <option value="AzodynPea.vpz">Pea</option> + <option value="AzodynWheat.vpz">Wheat</option> + <option value="AzodynBarley.vpz">Barley</option> + </param> + </inputs> + <outputs> + <data format="csv" name="inputs" label="Azodyn default inputs"/> + <data format="csv" name="outputs" label="Azodyn default outputs"/> + </outputs> + <tests> + <test> + <param name="crop_type" value="AzodynPea.vpz" /> + <output name="inputs"> + <assert_contents> + <has_text text="simulation_engine.duration;simulation_engine.begin" /> + <has_text text="Breteniere_1991_2018.csv;AZODYN" /> + </assert_contents> + </output> + <output name="outputs"> + <assert_contents> + <has_text text="id;path;integration" /> + <has_text text="Des_cumul;view/AzodynPea:Frost.Des_cumul;all" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Azodyn crop models default inputs and outputs provider + +Full documentation is available here : https://siwaa.toulouse.inrae.fr/ in section "Tool Tuto > Azodyn tool" +]]> + </help> +</tool> +