3
+ − 1 <tool id="insect_phenology_model" name="Insect phenology model" version="1.1.0">
0
+ − 2 <description>expressing stage-specific phenology and population dynamics</description>
+ − 3 <requirements>
4
+ − 4 <requirement type="package" version="1.4.4">r-optparse</requirement>
0
+ − 5 </requirements>
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+ − 6 <command detect_errors="exit_code"><![CDATA[
0
+ − 7 Rscript '$__tool_directory__/insect_phenology_model.R'
+ − 8 -a $adult_mort
+ − 9 -b $adult_accum
+ − 10 -c $egg_mort
2
+ − 11 -e '$location'
0
+ − 12 -f $max_clutch_size
+ − 13 -i $min_clutch_size
+ − 14 -j $nymph_mort
+ − 15 -k $old_nymph_accum
3
+ − 16 -n $input.metadata.data_lines
2
+ − 17 -o '$output'
0
+ − 18 -p $oviposition
+ − 19 -q $photoperiod
+ − 20 -s $replications
+ − 21 -t $se_plot
3
+ − 22 -v '$input'
5
+ − 23 -y $young_nymph_accum
+ − 24 -x '$insect']]></command>
0
+ − 25 <inputs>
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+ − 26 <param name="input" type="data" format="csv" label="Temperature data" />
2
+ − 27 <param name="location" type="text" value="" optional="false" label="Location" />
5
+ − 28 <param name="insect" type="select" label="Select insect">
+ − 29 <option value="Brown Marmolated Stink Bug" selected="True">Brown Marmolated Stink Bug</option>
+ − 30 </param>
0
+ − 31 <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
+ − 32 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
+ − 33 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
+ − 34 <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
+ − 35 <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
+ − 36 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
+ − 37 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
+ − 38 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
+ − 39 <param name="young_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (egg->young nymph)" />
+ − 40 <param name="old_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (young nymph->old nymph)" />
+ − 41 <param name="adult_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (old nymph->adult)" />
+ − 42 <param name="se_plot" type="select" label="Plot SE?">
+ − 43 <option value="1" selected="True">Yes</option>
+ − 44 <option value="0">No</option>
+ − 45 </param>
+ − 46 </inputs>
+ − 47 <outputs>
3
+ − 48 <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" />
0
+ − 49 </outputs>
+ − 50 <tests>
+ − 51 <test>
3
+ − 52 <param name="input" value="state_college.csv" ftype="csv" />
+ − 53 <param name="location" value="State College PA" />
+ − 54 <param name="replications" value="10" />
0
+ − 55 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
+ − 56 </test>
+ − 57 </tests>
+ − 58 <help>
+ − 59 **What it does**
+ − 60
+ − 61 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
+ − 62
+ − 63 -----
+ − 64
+ − 65 **Required options**
+ − 66
+ − 67 * **Location** - the location associated with the selected temperature data.
+ − 68 * **Temperature data** - select the dataset from your history containing the temperature data.
+ − 69 * **Number of replications** - number of replications.
+ − 70 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
+ − 71 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
+ − 72 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
+ − 73 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
+ − 74 * **Adjustment oviposition rate** - adjustment oviposition rate.
+ − 75 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
+ − 76 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
+ − 77 * **Adjustment of DD accumulation (egg->young nymph)** - adjustment of DD accumulation (egg->young nymph).
+ − 78 * **Adjustment of DD accumulation (young nymph->old nymph)** - adjustment of DD accumulation (young nymph->old nymph).
+ − 79 * **Adjustment of DD accumulation (old nymph->adult)** - adjustment of DD accumulation (old nymph->adult).
+ − 80 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
+ − 81
+ − 82 </help>
+ − 83 <citations>
+ − 84 <citation type="doi">10.3389/fphys.2016.00165</citation>
3
+ − 85 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
+ − 86 <citation type="doi">10.7289/V5D21VHZ</citation>
0
+ − 87 </citations>
+ − 88 </tool>