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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 $life_stages.append("Adult")
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18 #end if
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13
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19 #if str($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 $life_stages.append("Total")
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13
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21 #end if
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17
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22 #set life_stages = ",".join($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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6
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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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9
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34 #end if
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17
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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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26
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49 --young_nymph_accumulation $young_nymph_accumulation
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29
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50 --output '$output'
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51 &>ipm_log.txt;
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52 if [[ $? -ne 0 ]]; then
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53 cp ipm_log.txt '$output';
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54 exit 1;
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55 fi]]></command>
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0
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56 <inputs>
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57 <param name="input" type="data" format="csv" label="Temperature data" />
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2
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58 <param name="location" type="text" value="" optional="false" label="Location" />
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5
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59 <param name="insect" type="select" label="Select insect">
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9
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60 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
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5
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61 </param>
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9
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62 <param name="replications" type="integer" value="10" min="2" label="Number of replications" />
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6
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63 <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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64 <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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65 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
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66 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
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67 <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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68 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
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69 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
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70 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
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6
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71 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" />
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72 <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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73 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" />
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74 <param name="plot_generations_separately" type="select" label="Plot generations separately?">
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75 <option value="yes" selected="True">Yes</option>
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76 <option value="no">No</option>
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77 </param>
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78 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">
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79 <option value="yes" selected="true">Yes</option>
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80 <option value="no">No</option>
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81 </param>
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82 <conditional name="plot_nymph_life_stage_cond">
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83 <param name="plot_nymph_life_stage" type="select" label="Plot nymph life stage?">
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84 <option value="yes" selected="true">Yes</option>
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85 <option value="no">No</option>
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9
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86 </param>
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87 <when value="yes">
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88 <param name="life_stages_nymph" type="select" multiple="true" label="Select nymph life stage">
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89 <option value="Total" selected="true">All</option>
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90 <option value="Young">Young</option>
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91 <option value="Old">Old</option>
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92 </param>
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93 </when>
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94 <when value="no"/>
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95 </conditional>
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96 <conditional name="plot_adult_life_stage_cond">
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97 <param name="plot_adult_life_stage" type="select" label="Plot adult life stage?">
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98 <option value="yes" selected="true">Yes</option>
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99 <option value="no">No</option>
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100 </param>
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101 <when value="yes">
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102 <param name="life_stages_adult" type="select" multiple="true" label="Select adult life stage">
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103 <option value="Total" selected="true">All</option>
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104 <option value="Pre-vittelogenic">Pre-vittelogenic</option>
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105 <option value="Vittelogenic">Vittelogenic</option>
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106 <option value="Diapausing">Diapausing</option>
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107 </param>
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108 </when>
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109 <when value="no"/>
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110 </conditional>
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111 <param name="plot_std_error" type="select" label="Plot standard error?">
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112 <option value="yes" selected="True">Yes</option>
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113 <option value="no">No</option>
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114 </param>
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115 </inputs>
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116 <outputs>
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117 <data name="output" format="csv" label="${tool.name} (analyzed data) on ${on_string}"/>
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118 <collection name="output_collection" type="list" label="${tool.name} (plots), on ${on_string}">
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119 <discover_datasets pattern="__name__" directory="output_dir" format="pdf" />
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120 </collection>
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121 </outputs>
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122 <tests>
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123 <test>
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3
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124 <param name="input" value="state_college.csv" ftype="csv" />
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125 <param name="location" value="State College PA" />
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12
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126 <param name="replications" value="2" />
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22
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127 <param name="plot_generations_separately" value="no" />
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128 <param name="plot_egg_life_stage" value="no" />
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129 <param name="life_stages_nymph" value="Young" />
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130 <param name="life_stages_adult" value="Pre-vittelogenic" />
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131 <output name="output" file="output1.csv" ftype="csv" compare="contains"/>
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132 <output_collection name="output_collection" type="list">
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133 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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134 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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135 </output_collection>
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136 </test>
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137 <test>
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138 <param name="input" value="state_college.csv" ftype="csv" />
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139 <param name="location" value="State College PA" />
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140 <param name="replications" value="2" />
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141 <param name="plot_generations_separately" value="no" />
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142 <output name="output" file="output2.csv" ftype="csv" compare="contains"/>
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143 <output_collection name="output_collection" type="list">
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144 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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145 <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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146 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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147 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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148 </output_collection>
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149 </test>
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150 <test>
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151 <param name="input" value="state_college.csv" ftype="csv" />
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152 <param name="location" value="State College PA" />
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153 <param name="replications" value="2" />
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154 <param name="plot_egg_life_stage" value="no" />
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155 <param name="life_stages_nymph" value="Old" />
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156 <param name="plot_adult_life_stage" value="no" />
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157 <output name="output" file="output3.csv" ftype="csv" compare="contains"/>
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158 <output_collection name="output_collection" type="list">
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159 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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160 </output_collection>
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161 </test>
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162 <test>
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163 <param name="input" value="state_college.csv" ftype="csv" />
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164 <param name="location" value="State College PA" />
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165 <param name="replications" value="2" />
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166 <output name="output" file="output4.csv" ftype="csv" compare="contains"/>
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167 <output_collection name="output_collection" type="list">
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168 <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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169 <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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170 <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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171 <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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172 </output_collection>
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173 </test>
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174 </tests>
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175 <help>
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176 **What it does**
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177
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178 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
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179
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180 -----
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181
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182 **Required options**
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183
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184 * **Location** - the location associated with the selected temperature data.
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185 * **Temperature data** - select the dataset from your history containing the temperature data.
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186 * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed.
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187 * **Number of replications** - number of replications.
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188 * **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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189 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
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190 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
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191 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
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192 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
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193 * **Adjustment oviposition rate** - adjustment oviposition rate.
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194 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
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195 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
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196 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
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197 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
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198 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
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199 * **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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200 * **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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201 * **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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202
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203 * **Select nymph life stage** - select the nymph life stage for plotting.
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204
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205 * **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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206
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207 * **Select adult life stage** - select the adult life stage for plotting.
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208
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209 * **Plot standard error** - add standard error lines to plot.
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210 </help>
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211 <citations>
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212 <citation type="doi">10.3389/fphys.2016.00165</citation>
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213 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
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214 <citation type="doi">10.7289/V5D21VHZ</citation>
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215 </citations>
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216 </tool>
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