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1 <tool id="insect_phenology_model" name="Insect phenology model" version="1.1.0">
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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
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4 <requirement type="package" version="1.4.4">r-optparse</requirement>
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0
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5 </requirements>
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2
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6 <command detect_errors="exit_code"><![CDATA[
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17
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7 #set life_stages = list()
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13
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8 #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage
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9 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage
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17
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10 #if str($plot_egg_life_stage) == "yes":
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11 $life_stages.append("Egg")
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12 #end if
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13 #if str($plot_nymph_life_stage) == "yes":
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14 $life_stages.append("Nymph")
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15 #end if
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16 #if str($plot_adult_life_stage) == "yes":
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17 $life_stages.append("Adult")
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18 #end if
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19 #if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes":
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17
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20 $life_stages.append("Total")
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21 #end if
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22 #set life_stages = ",".join($life_stages)
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23 mkdir output_dir &&
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24 Rscript '$__tool_directory__/insect_phenology_model.R'
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25 --adult_mortality $adult_mortality
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26 --adult_accumulation $adult_accumulation
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27 --egg_mortality $egg_mortality
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28 --input '$input'
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29 --insect '$insect'
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30 --insects_per_replication $insects_per_replication
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17
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31 --life_stages '$life_stages'
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32 #if str($plot_adult_life_stage) == "yes":
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33 --life_stages_adult '$plot_adult_life_stage_cond.life_stages_adult'
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34 #end if
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35 #if str($plot_nymph_life_stage) == "yes":
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36 --life_stages_nymph '$plot_nymph_life_stage_cond.life_stages_nymph'
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9
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37 #end if
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6
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38 --location '$location'
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39 --max_clutch_size $max_clutch_size
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40 --min_clutch_size $min_clutch_size
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41 --nymph_mortality $nymph_mortality
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42 --num_days $input.metadata.data_lines
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43 --old_nymph_accumulation $old_nymph_accumulation
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44 --oviposition $oviposition
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45 --photoperiod $photoperiod
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46 --replications $replications
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47 --plot_generations_separately $plot_generations_separately
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48 --plot_std_error $plot_std_error
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49 --young_nymph_accumulation $young_nymph_accumulation]]></command>
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50 <inputs>
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51 <param name="input" type="data" format="csv" label="Temperature data" />
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2
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52 <param name="location" type="text" value="" optional="false" label="Location" />
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5
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53 <param name="insect" type="select" label="Select insect">
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54 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
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5
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55 </param>
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56 <param name="replications" type="integer" value="10" min="2" label="Number of replications" />
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57 <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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0
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58 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
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6
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59 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
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60 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
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61 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
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0
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62 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
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63 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
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64 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
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65 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" />
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66 <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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67 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" />
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68 <param name="plot_generations_separately" type="select" label="Plot generations separately?">
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69 <option value="yes" selected="True">Yes</option>
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70 <option value="no">No</option>
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71 </param>
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72 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">
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73 <option value="yes" selected="true">Yes</option>
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74 <option value="no">No</option>
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75 </param>
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76 <conditional name="plot_nymph_life_stage_cond">
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77 <param name="plot_nymph_life_stage" type="select" label="Plot nymph life stage?">
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78 <option value="yes" selected="true">Yes</option>
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79 <option value="no">No</option>
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80 </param>
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81 <when value="yes">
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82 <param name="life_stages_nymph" type="select" multiple="true" label="Select nymph life stage">
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83 <option value="Total" selected="true">All</option>
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84 <option value="Young">Young</option>
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85 <option value="Old">Old</option>
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86 </param>
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87 </when>
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88 <when value="no"/>
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89 </conditional>
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90 <conditional name="plot_adult_life_stage_cond">
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91 <param name="plot_adult_life_stage" type="select" label="Plot adult life stage?">
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92 <option value="yes" selected="true">Yes</option>
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93 <option value="no">No</option>
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94 </param>
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95 <when value="yes">
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96 <param name="life_stages_adult" type="select" multiple="true" label="Select adult life stage">
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97 <option value="Total" selected="true">All</option>
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98 <option value="Pre-vittelogenic">Pre-vittelogenic</option>
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99 <option value="Vittelogenic">Vittelogenic</option>
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100 <option value="Diapausing">Diapausing</option>
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101 </param>
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102 </when>
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103 <when value="no"/>
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104 </conditional>
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105 <param name="plot_std_error" type="select" label="Plot standard error?">
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106 <option value="yes" selected="True">Yes</option>
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107 <option value="no">No</option>
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108 </param>
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109 </inputs>
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110 <outputs>
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111 <collection name="output_collection" type="list" label="${tool.name} ${location}, on ${on_string}">
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112 <discover_datasets pattern="__name__" directory="output_dir" format="pdf" />
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113 </collection>
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114 </outputs>
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115 <tests>
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116 <test>
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117 <param name="input" value="state_college.csv" ftype="csv" />
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118 <param name="location" value="State College PA" />
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119 <param name="replications" value="2" />
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120 <output_collection name="output_collection" type="list">
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121 <element name="01_egg_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/>
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122 <element name="04_total_nymph_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/>
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123 <element name="08_total_adult_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/>
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124 <element name="09_total_pop_by_generation.pdf" file="pop_by_generation.pdf" ftype="pdf" compare="contains"/>
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125 </output_collection>
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126 </test>
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127 </tests>
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128 <help>
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129 **What it does**
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130
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131 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
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132
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133 -----
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134
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135 **Required options**
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136
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137 * **Location** - the location associated with the selected temperature data.
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138 * **Temperature data** - select the dataset from your history containing the temperature data.
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139 * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed.
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140 * **Number of replications** - number of replications.
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141 * **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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142 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
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143 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
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144 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
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145 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
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146 * **Adjustment oviposition rate** - adjustment oviposition rate.
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147 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
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148 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
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149 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
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150 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
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151 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
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152 * **Plot generations separately** - select "Yes" to plot P, F1 and F2 as separate lines or "no" to pool across generations, resulting in a total for the selected life states.
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153 * **Plot egg life stage** - select "Yes" to plot the egg life stage. If all life stages (egg, nymph and adult) are selected for plotting, one output for the total will be produced.
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154 * **Plot nymph life stage** - select "Yes" to plot the nymph life stage. If all life stages (egg, nymph and adult) are selected for plotting, one output for the total will be produced.
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155
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156 * **Select nymph life stage** - select the nymph life stage for plotting.
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157
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158 * **Plot adult life stage** - select "Yes" to plot the adult life stage. If all life stages (egg, nymph and adult) are selected for plotting, one output for the total will be produced.
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159
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160 * **Select adult life stage** - select the adult life stage for plotting.
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161
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162 * **Plot standard error** - add standard error lines to plot.
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163 </help>
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164 <citations>
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165 <citation type="doi">10.3389/fphys.2016.00165</citation>
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166 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
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167 <citation type="doi">10.7289/V5D21VHZ</citation>
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168 </citations>
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169 </tool>
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