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+ − 1 <tool id="insect_phenology_model" name="Insect phenology model" version="1.1.0">
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+ − 2 <description>expressing stage-specific phenology and population dynamics</description>
+ − 3 <requirements>
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+ − 4 <requirement type="package" version="1.4.4">r-optparse</requirement>
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+ − 5 </requirements>
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+ − 6 <command detect_errors="exit_code"><![CDATA[
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+ − 7 Rscript '$__tool_directory__/insect_phenology_model.R'
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+ − 8 --adult_mortality $adult_mortality
+ − 9 --adult_accumulation $adult_accumulation
+ − 10 --egg_mortality $egg_mortality
+ − 11 --input '$input'
+ − 12 --insect '$insect'
+ − 13 --insects_per_replication $insects_per_replication
+ − 14 --location '$location'
+ − 15 --max_clutch_size $max_clutch_size
+ − 16 --min_clutch_size $min_clutch_size
+ − 17 --nymph_mortality $nymph_mortality
+ − 18 --num_days $input.metadata.data_lines
+ − 19 --old_nymph_accumulation $old_nymph_accumulation
+ − 20 --output '$output'
+ − 21 --oviposition $oviposition
+ − 22 --photoperiod $photoperiod
+ − 23 --replications $replications
+ − 24 --std_error_plot $std_error_plot
+ − 25 --young_nymph_accumulation $young_nymph_accumulation]]></command>
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+ − 26 <inputs>
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+ − 27 <param name="input" type="data" format="csv" label="Temperature data" />
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+ − 28 <param name="location" type="text" value="" optional="false" label="Location" />
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+ − 29 <param name="insect" type="select" label="Select insect">
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+ − 30 <option value="Brown Marmorated Stink Bug" selected="True">Brown Marmorated Stink Bug</option>
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+ − 31 </param>
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+ − 32 <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
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+ − 33 <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication" />
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+ − 34 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
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+ − 35 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
+ − 36 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
+ − 37 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
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+ − 38 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
+ − 39 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
+ − 40 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
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+ − 41 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" />
+ − 42 <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" />
+ − 43 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" />
+ − 44 <param name="std_error_plot" type="select" label="Plot standard error?">
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+ − 45 <option value="1" selected="True">Yes</option>
+ − 46 <option value="0">No</option>
+ − 47 </param>
+ − 48 </inputs>
+ − 49 <outputs>
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+ − 50 <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" />
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+ − 51 </outputs>
+ − 52 <tests>
+ − 53 <test>
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+ − 54 <param name="input" value="state_college.csv" ftype="csv" />
+ − 55 <param name="location" value="State College PA" />
+ − 56 <param name="replications" value="10" />
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+ − 57 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
+ − 58 </test>
+ − 59 </tests>
+ − 60 <help>
+ − 61 **What it does**
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+ − 62
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+ − 63 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
+ − 64
+ − 65 -----
+ − 66
+ − 67 **Required options**
+ − 68
+ − 69 * **Location** - the location associated with the selected temperature data.
+ − 70 * **Temperature data** - select the dataset from your history containing the temperature data.
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+ − 71 * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed.
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+ − 72 * **Number of replications** - number of replications.
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+ − 73 * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects.
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+ − 74 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
+ − 75 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
+ − 76 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
+ − 77 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
+ − 78 * **Adjustment oviposition rate** - adjustment oviposition rate.
+ − 79 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
+ − 80 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
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+ − 81 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
+ − 82 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
+ − 83 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
+ − 84 * **Plot standard error** - add standard error lines to plot.
+ − 85
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+ − 86 </help>
+ − 87 <citations>
+ − 88 <citation type="doi">10.3389/fphys.2016.00165</citation>
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+ − 89 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
+ − 90 <citation type="doi">10.7289/V5D21VHZ</citation>
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+ − 91 </citations>
+ − 92 </tool>