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<tool id="insect_phenology_model" name="Insect phenology model" version="1.1.0">
    <description>expressing stage-specific phenology and population dynamics</description>
    <requirements>
        <requirement type="package" version="1.4.4">r-optparse</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/insect_phenology_model.R'
-a $adult_mort
-b $adult_accum
-c $egg_mort
-e '$location'
-f $max_clutch_size
-i $min_clutch_size
-j $nymph_mort
-k $old_nymph_accum
-n $input.metadata.data_lines
-o '$output'
-p $oviposition
-q $photoperiod
-s $replications
-t $se_plot
-v '$input'
-y $young_nymph_accum]]></command>
    <inputs>
        <param name="input" type="data" format="csv" label="Temperature data" />
        <param name="location" type="text" value="" optional="false" label="Location" />
        <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
        <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
        <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
        <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
        <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
        <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
        <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
        <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
        <param name="young_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (egg->young nymph)" />
        <param name="old_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (young nymph->old nymph)" />
        <param name="adult_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (old nymph->adult)" />
        <param name="se_plot" type="select" label="Plot SE?">
            <option value="1" selected="True">Yes</option>
            <option value="0">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="state_college.csv" ftype="csv" />
            <param name="location" value="State College PA" />
            <param name="replications" value="10" />
            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
        </test>
    </tests>
    <help>
**What it does**
 
Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.

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**Required options**

 * **Location** - the location associated with the selected temperature data.
 * **Temperature data** - select the dataset from your history containing the temperature data.
 * **Number of replications** - number of replications.
 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
 * **Adjustment oviposition rate** - adjustment oviposition rate.
 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
 * **Adjustment of DD accumulation (egg->young nymph)** - adjustment of DD accumulation (egg->young nymph).
 * **Adjustment of DD accumulation (young nymph->old nymph)** - adjustment of DD accumulation (young nymph->old nymph).
 * **Adjustment of DD accumulation (old nymph->adult)** - adjustment of DD accumulation (old nymph->adult).
 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
 
    </help>
    <citations>
        <citation type="doi">10.3389/fphys.2016.00165</citation>
        <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
        <citation type="doi">10.7289/V5D21VHZ</citation>
    </citations>
</tool>