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1 <?xml version="."?>
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2 <tool id="insect_phenology_model" name="Insect phenology model" version="1.0.0">
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3 <description>expressing stage-specific phenology and population dynamics</description>
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4 <requirements>
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5 <requirement type="package" version="1.3.0">r-optparse</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 #set loc_lat_items = $location.split(':')
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1
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9 #set loc = $loc_lat_items[0]
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10 $set lat = $loc_lat_items[1]
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0
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11 Rscript '$__tool_directory__/insect_phenology_model.R'
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12 -a $adult_mort
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13 -b $adult_accum
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14 -c $egg_mort
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15 -d $lat
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16 -e $loc
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17 -f $max_clutch_size
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18 -i $min_clutch_size
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19 -j $nymph_mort
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20 -k $old_nymph_accum
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21 -o $output
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22 -p $oviposition
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23 -q $photoperiod
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24 -s $replications
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25 -t $se_plot
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26 -u $year
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27 -v '$temperature_data'
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28 -y $young_nymph_accum
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29 ]]></command>
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30 <inputs>
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31 <param name="location" type="select" label="Location">
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32 <options from_file="locations.txt">
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33 <column name="name" index="0"/>
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34 <column name="value" index="1"/>
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35 </options>
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36 </param>
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37 <param name="temperature_data" type="data" format="csv" label="Temperature data" />
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38 <param name="year" type="select" label="Temperature data year">
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39 <options from_file="years.txt">
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40 <column name="name" index="0"/>
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41 <column name="value" index="1"/>
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42 </options>
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43 </param>
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44 <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
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45 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
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46 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
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47 <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
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48 <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
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49 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
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50 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
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51 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
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52 <param name="young_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (egg->young nymph)" />
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53 <param name="old_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (young nymph->old nymph)" />
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54 <param name="adult_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (old nymph->adult)" />
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55 <param name="se_plot" type="select" label="Plot SE?">
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56 <option value="1" selected="True">Yes</option>
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57 <option value="0">No</option>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data name="output" format="pdf" label="${tool.name} ${location}:${year} on ${on_string}" />
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="temperature_data" value="asheville2014.csv" ftype="csv" />
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66 <param name="location" value="asheville:35.58" />
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67 <param name="year" value="2014" />
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68 <param name="replications" value="3" />
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69 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
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70 </test>
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71 </tests>
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72 <help>
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73 **What it does**
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74
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75 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
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76
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77 -----
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78
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79 **Required options**
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80
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81 * **Location** - the location associated with the selected temperature data.
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82 * **Temperature data** - select the dataset from your history containing the temperature data.
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83 * **Temperature data year** - the year during which the temperature data was recorded.
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84 * **Number of replications** - number of replications.
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85 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
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86 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
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87 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
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88 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
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89 * **Adjustment oviposition rate** - adjustment oviposition rate.
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90 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
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91 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
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92 * **Adjustment of DD accumulation (egg->young nymph)** - adjustment of DD accumulation (egg->young nymph).
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93 * **Adjustment of DD accumulation (young nymph->old nymph)** - adjustment of DD accumulation (young nymph->old nymph).
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94 * **Adjustment of DD accumulation (old nymph->adult)** - adjustment of DD accumulation (old nymph->adult).
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95 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
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96
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97 </help>
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98 <citations>
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99 <citation type="doi">10.3389/fphys.2016.00165</citation>
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100 </citations>
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101 </tool>
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