Mercurial > repos > greg > insect_phenology_model
changeset 42:64132300c62e draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 23 Apr 2018 09:48:58 -0400 |
| parents | f4d683709b7f |
| children | fd3c00392fce |
| files | insect_phenology_model.xml |
| diffstat | 1 files changed, 77 insertions(+), 45 deletions(-) [+] |
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--- a/insect_phenology_model.xml Wed Apr 11 13:26:56 2018 -0400 +++ b/insect_phenology_model.xml Mon Apr 23 09:48:58 2018 -0400 @@ -30,7 +30,10 @@ --adult_mortality $adult_mortality --adult_accumulation $adult_accumulation --egg_mortality $egg_mortality ---input_ytd '$input_ytd' +#if str($merge_ytd_temperature_data_cond.merge_ytd_temperature_data) == "yes": + --input_ytd '$merge_ytd_temperature_data_cond.input_ytd' + --num_days_ytd $input_ytd.metadata.data_lines +#end if --input_norm '$input_norm' --insect '$insect' --insects_per_replication $insects_per_replication @@ -45,7 +48,6 @@ --max_clutch_size $max_clutch_size --min_clutch_size $min_clutch_size --nymph_mortality $nymph_mortality ---num_days_ytd $input_ytd.metadata.data_lines --old_nymph_accumulation $old_nymph_accumulation --oviposition $oviposition --photoperiod $photoperiod @@ -59,28 +61,37 @@ exit 1; fi]]></command> <inputs> - <param name="input_ytd" type="data" format="csv" label="Year-to-date temperature data"> - <validator type="expression" message="Year-to-date temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator> - </param> <param name="input_norm" type="data" format="csv" label="30 year normals temperature data"> <validator type="expression" message="30 year normals temperature data must have 10 columns and 366 rows">value is not None and value.metadata.columns==10 and value.metadata.data_lines==366</validator> </param> - <param name="location" type="text" value="" optional="false" label="Location" /> + <conditional name="merge_ytd_temperature_data_cond"> + <param name="merge_ytd_temperature_data" type="select" label="Merge year-to-date temperature data with 30 year normals temperature data?"> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="input_ytd" type="data" format="csv" label="Year-to-date temperature data"> + <validator type="expression" message="Year-to-date temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator> + </param> + </when> + <when value="no"/> + </conditional> + <param name="location" type="text" value="" optional="false" label="Location"/> <param name="insect" type="select" label="Select insect"> <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option> </param> - <param name="replications" type="integer" value="10" min="2" label="Number of replications" /> - <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication" /> - <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> - <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> - <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> - <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> - <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" /> - <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" /> - <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" /> - <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" /> - <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" /> - <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" /> + <param name="replications" type="integer" value="10" min="2" label="Number of replications"/> + <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication"/> + <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination"/> + <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality"/> + <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality"/> + <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality"/> + <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate"/> + <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size"/> + <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size"/> + <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)"/> + <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)"/> + <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)"/> <param name="plot_generations_separately" type="select" label="Plot generations separately?"> <option value="yes" selected="True">Yes</option> <option value="no">No</option> @@ -125,22 +136,22 @@ </inputs> <outputs> <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}"> - <discover_datasets pattern="__name__" directory="output_data_dir" format="csv" /> + <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/> </collection> <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}"> - <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf" /> + <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/> </collection> </outputs> <tests> <test> - <param name="input_ytd" value="state_college_partial.csv" ftype="csv" /> - <param name="input_norm" value="30_year_normals.csv" ftype="csv" /> - <param name="location" value="State College PA" /> - <param name="replications" value="2" /> - <param name="plot_generations_separately" value="no" /> - <param name="plot_egg_life_stage" value="no" /> - <param name="life_stages_nymph" value="Young" /> - <param name="life_stages_adult" value="Pre-vittelogenic" /> + <param name="input_norm" value="30_year_normals.csv" ftype="csv"/> + <param name="merge_ytd_temperature_data" value="no"/> + <param name="location" value="State College PA"/> + <param name="replications" value="2"/> + <param name="plot_generations_separately" value="no"/> + <param name="plot_egg_life_stage" value="no"/> + <param name="life_stages_nymph" value="Young"/> + <param name="life_stages_adult" value="Pre-vittelogenic"/> <output_collection name="output_data_collection" type="list"> <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/> </output_collection> @@ -150,11 +161,28 @@ </output_collection> </test> <test> - <param name="input_ytd" value="state_college_ytd.csv" ftype="csv" /> - <param name="input_norm" value="30_year_normals.csv" ftype="csv" /> - <param name="location" value="State College PA" /> - <param name="replications" value="2" /> - <param name="plot_generations_separately" value="no" /> + <param name="input_norm" value="30_year_normals.csv" ftype="csv"/> + <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/> + <param name="location" value="State College PA"/> + <param name="replications" value="2"/> + <param name="plot_generations_separately" value="no"/> + <param name="plot_egg_life_stage" value="no"/> + <param name="life_stages_nymph" value="Young"/> + <param name="life_stages_adult" value="Pre-vittelogenic"/> + <output_collection name="output_data_collection" type="list"> + <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/> + </output_collection> + <output_collection name="output_plots_collection" type="list"> + <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> + </output_collection> + </test> + <test> + <param name="input_norm" value="30_year_normals.csv" ftype="csv"/> + <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/> + <param name="location" value="State College PA"/> + <param name="replications" value="2"/> + <param name="plot_generations_separately" value="no"/> <output_collection name="output_data_collection" type="list"> <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/> </output_collection> @@ -166,13 +194,13 @@ </output_collection> </test> <test> - <param name="input_ytd" value="state_college_partial.csv" ftype="csv" /> - <param name="input_norm" value="30_year_normals.csv" ftype="csv" /> - <param name="location" value="State College PA" /> - <param name="replications" value="2" /> - <param name="plot_egg_life_stage" value="no" /> - <param name="life_stages_nymph" value="Old" /> - <param name="plot_adult_life_stage" value="no" /> + <param name="input_norm" value="30_year_normals.csv" ftype="csv"/> + <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/> + <param name="location" value="State College PA"/> + <param name="replications" value="2"/> + <param name="plot_egg_life_stage" value="no"/> + <param name="life_stages_nymph" value="Old"/> + <param name="plot_adult_life_stage" value="no"/> <output_collection name="output_data_collection" type="list"> <element name="01_generation_P.csv" file="output_p_3.csv" ftype="csv" compare="contains"/> <element name="02_generation_F1.csv" file="output_f1_3.csv" ftype="csv" compare="contains"/> @@ -184,10 +212,10 @@ </output_collection> </test> <test> - <param name="input_ytd" value="state_college_ytd.csv" ftype="csv" /> - <param name="input_norm" value="30_year_normals.csv" ftype="csv" /> - <param name="location" value="State College PA" /> - <param name="replications" value="2" /> + <param name="input_norm" value="30_year_normals.csv" ftype="csv"/> + <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/> + <param name="location" value="State College PA"/> + <param name="replications" value="2"/> <output_collection name="output_data_collection" type="list"> <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/> <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/> @@ -211,8 +239,12 @@ **Required options** + * **30 year normals temperature data** - the dataset from your history containing the 30-year normals temperature data (available at http://pestwatch.psu.edu/ghcn). + * **Merge year-to-date temperature data with 30 year normals temperature data** - select Yes to merge a year-to-date temperature dataset from your history into the selected 30 year normals temperature data. + + * **Year-to-date temperature data** - the dataset from your history containing the year-to-date temperature data (available at http://pestwatch.psu.edu/minmax). + * **Location** - the location associated with the selected temperature data. - * **Temperature data** - select the dataset from your history containing the temperature data. * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed. * **Number of replications** - number of replications. * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects.