comparison insect_phenology_model.xml @ 42:64132300c62e draft

Uploaded

41:f4d683709b7f

mkdir output_plots_dir &&
Rscript '$__tool_directory__/insect_phenology_model.R'
--adult_mortality $adult_mortality
--adult_accumulation $adult_accumulation
--egg_mortality $egg_mortality
--input_ytd '$input_ytd'
--input_norm '$input_norm'
--insect '$insect'
--insects_per_replication $insects_per_replication
--life_stages '$life_stages'
#if str($plot_adult_life_stage) == "yes":

#end if
--location '$location'
--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
--replications $replications
--plot_generations_separately $plot_generations_separately

if [[ $? -ne 0 ]]; then
    cp ipm_log.txt '$error_file';
    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" />
        <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="plot_generations_separately" type="select" label="Plot generations separately?">
            <option value="yes" selected="True">Yes</option>
            <option value="no">No</option>
        </param>
        <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">

            <option value="no">No</option>
        </param>
    </inputs>
    <outputs>
        <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_data_dir" format="csv" />
        </collection>
        <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf" />
        </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" />
            <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_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" />
            <output_collection name="output_data_collection" type="list">
                <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/>
            </output_collection>
            <output_collection name="output_plots_collection" type="list">
                <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>

                <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
                <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
            </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" />
            <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"/>
                <element name="03_generation_F2.csv" file="output_f2_3.csv" ftype="csv" compare="contains"/>
                <element name="04_combined_generations.csv" file="output_combined3.csv" ftype="csv" compare="contains"/>

            <output_collection name="output_plots_collection" type="list">
                <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
            </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" />
            <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"/>
                <element name="03_generation_F2.csv" file="output_f2_4.csv" ftype="csv" compare="contains"/>
                <element name="04_combined_generations.csv" file="output_combined4.csv" ftype="csv" compare="contains"/>

-----

**Required options**

 * **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.
 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.

42:64132300c62e

mkdir output_plots_dir &&
Rscript '$__tool_directory__/insect_phenology_model.R'
--adult_mortality $adult_mortality
--adult_accumulation $adult_accumulation
--egg_mortality $egg_mortality
#if str($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 $insects_per_replication
--life_stages '$life_stages'
#if str($plot_adult_life_stage) == "yes":

#end if
--location '$location'
--max_clutch_size $max_clutch_size
--min_clutch_size $min_clutch_size
--nymph_mortality $nymph_mortality
--old_nymph_accumulation $old_nymph_accumulation
--oviposition $oviposition
--photoperiod $photoperiod
--replications $replications
--plot_generations_separately $plot_generations_separately

if [[ $? -ne 0 ]]; then
    cp ipm_log.txt '$error_file';
    exit 1;
fi]]></command>
    <inputs>
        <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>
        <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="plot_generations_separately" type="select" label="Plot generations separately?">
            <option value="yes" selected="True">Yes</option>
            <option value="no">No</option>
        </param>
        <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">

            <option value="no">No</option>
        </param>
    </inputs>
    <outputs>
        <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/>
        </collection>
        <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <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>
            <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_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>
            <output_collection name="output_plots_collection" type="list">
                <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>

                <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
                <element name="09_total_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_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"/>
                <element name="03_generation_F2.csv" file="output_f2_3.csv" ftype="csv" compare="contains"/>
                <element name="04_combined_generations.csv" file="output_combined3.csv" ftype="csv" compare="contains"/>

            <output_collection name="output_plots_collection" type="list">
                <element name="03_old_nymph_pop_by_generation.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"/>
            <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"/>
                <element name="03_generation_F2.csv" file="output_f2_4.csv" ftype="csv" compare="contains"/>
                <element name="04_combined_generations.csv" file="output_combined4.csv" ftype="csv" compare="contains"/>

-----

**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.
 * **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.
 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.