comparison insect_phenology_model.xml @ 37:b7dcecf5476a draft

Uploaded

36:5097cfeedc4f

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

#end if
--location '$location'
--max_clutch_size $max_clutch_size
--min_clutch_size $min_clutch_size
--nymph_mortality $nymph_mortality
--num_days $input.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" type="data" format="csv" label="Temperature data" />
        <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" />

            <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="state_college.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" />

                <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" value="state_college.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"/>

                <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" value="state_college.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_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" value="state_college.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"/>

37:b7dcecf5476a

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($plot_adult_life_stage) == "yes":
    --life_stages_adult '$plot_adult_life_stage_cond.life_stages_adult'

#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" />

            <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input_ytd" value="state_college.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" />

                <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.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"/>

                <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.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_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.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"/>