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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>
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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
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9 --adult_accumulation $adult_accumulation
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10 --egg_mortality $egg_mortality
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11 --input '$input'
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12 --insect '$insect'
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13 --insects_per_replication $insects_per_replication
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14 --location '$location'
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15 --max_clutch_size $max_clutch_size
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16 --min_clutch_size $min_clutch_size
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17 --nymph_mortality $nymph_mortality
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18 --num_days $input.metadata.data_lines
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19 --old_nymph_accumulation $old_nymph_accumulation
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20 --output '$output'
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21 --oviposition $oviposition
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22 --photoperiod $photoperiod
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23 --replications $replications
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24 --std_error_plot $std_error_plot
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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" />
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36 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
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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" />
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39 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
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40 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
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105
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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)" />
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42 <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" />
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43 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" />
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44 <param name="std_error_plot" type="select" label="Plot standard error?">
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45 <option value="1" selected="True">Yes</option>
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46 <option value="0">No</option>
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47 </param>
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48 </inputs>
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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>
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52 <tests>
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53 <test>
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54 <param name="input" value="state_college.csv" ftype="csv" />
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55 <param name="location" value="State College PA" />
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56 <param name="replications" value="10" />
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57 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
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58 </test>
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59 </tests>
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60 <help>
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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.
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64
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65 -----
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66
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67 **Required options**
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68
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69 * **Location** - the location associated with the selected temperature data.
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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.
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75 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
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76 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
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77 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
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78 * **Adjustment oviposition rate** - adjustment oviposition rate.
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79 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
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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).
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82 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
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83 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
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84 * **Plot standard error** - add standard error lines to plot.
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85
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86 </help>
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87 <citations>
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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>
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90 <citation type="doi">10.7289/V5D21VHZ</citation>
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91 </citations>
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92 </tool>
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