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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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42
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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 #import os
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8 #set output_data_dir = "output_data_dir"
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9 #set output_plots_dir = "output_plots_dir"
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10 #set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv")
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11 #set custom_date_interval = $custom_date_interval_cond.custom_date_interval
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12 #set life_stages = list()
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13 #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage
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14 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage
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15 #if str($plot_egg_life_stage) == "yes":
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16 $life_stages.append("Egg")
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17 #end if
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18 #if str($plot_nymph_life_stage) == "yes":
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19 $life_stages.append("Nymph")
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20 #end if
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21 #if str($plot_adult_life_stage) == "yes":
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22 $life_stages.append("Adult")
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23 #end if
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24 #if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes":
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25 $life_stages.append("Total")
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26 #end if
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27 #set life_stages = ",".join($life_stages)
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28 mkdir output_data_dir &&
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29 mkdir output_plots_dir &&
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30 Rscript '$__tool_directory__/insect_phenology_model.R'
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31 --adult_mortality $adult_mortality
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32 --adult_accumulation $adult_accumulation
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33 --egg_mortality $egg_mortality
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112
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34 #if str($merge_ytd_temperature_data_cond.merge_ytd_temperature_data) == "yes":
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35 --input_ytd '$merge_ytd_temperature_data_cond.input_ytd'
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36 --location '$merge_ytd_temperature_data_cond.location'
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37 --num_days_ytd $merge_ytd_temperature_data_cond.input_ytd.metadata.data_lines
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38 #end if
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39 --input_norm '$input_norm'
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40 --insect '$insect'
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41 --insects_per_replication $insects_per_replication
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42 --life_stages '$life_stages'
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43 #if str($plot_adult_life_stage) == "yes":
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44 --life_stages_adult '$plot_adult_life_stage_cond.life_stages_adult'
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45 #end if
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46 #if str($plot_nymph_life_stage) == "yes":
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47 --life_stages_nymph '$plot_nymph_life_stage_cond.life_stages_nymph'
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48 #end if
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49 --max_clutch_size $max_clutch_size
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50 --min_clutch_size $min_clutch_size
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51 --nymph_mortality $nymph_mortality
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52 --old_nymph_accumulation $old_nymph_accumulation
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53 --oviposition $oviposition
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54 --photoperiod $photoperiod
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55 --plot_generations_separately $plot_generations_separately
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56 --plot_std_error $plot_std_error
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57 --replications $replications
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58 #if str($custom_date_interval) == "yes":
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59 --start_date '$start_date'
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60 --end_date '$end_date'
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61 #end if
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62 --young_nymph_accumulation $young_nymph_accumulation
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63 &>ipm_log.txt;
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64 if [[ $? -ne 0 ]]; then
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65 cp ipm_log.txt '$error_file';
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66 exit 1;
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67 fi]]></command>
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68 <inputs>
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69 <param name="input_norm" type="data" format="csv" label="30 year normals temperature data">
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70 <validator type="expression" message="30 year normals temperature data must have 10 columns and 366 rows">value is not None and value.metadata.columns==10 and value.metadata.data_lines==366</validator>
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71 </param>
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72 <conditional name="merge_ytd_temperature_data_cond">
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73 <param name="merge_ytd_temperature_data" type="select" label="Merge year-to-date temperature data with 30 year normals temperature data?">
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74 <option value="yes" selected="true">Yes</option>
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75 <option value="no">No</option>
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76 </param>
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77 <when value="yes">
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78 <param name="input_ytd" type="data" format="csv" label="Year-to-date temperature data">
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79 <validator type="expression" message="Year-to-date temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator>
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80 </param>
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81 <param name="location" type="text" value="" optional="true" label="Location" help="Enter the location or leave blank to use the station name from 30 year normals data."/>
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82 </when>
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83 <when value="no"/>
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84 </conditional>
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86
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85 <param name="insect" type="select" label="Select insect">
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86 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
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86
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87 </param>
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112
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88 <param name="replications" type="integer" value="10" min="2" label="Number of replications"/>
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89 <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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90 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination"/>
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91 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality"/>
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92 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality"/>
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93 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality"/>
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94 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate"/>
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95 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size"/>
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96 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size"/>
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97 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)"/>
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98 <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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99 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)"/>
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100 <conditional name="custom_date_interval_cond">
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101 <param name="custom_date_interval" type="select" label="Set custom date interval for plots?">
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102 <option value="no" selected="true">No</option>
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103 <option value="yes">Yes</option>
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104 </param>
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105 <when value="no"/>
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106 <when value="yes">
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107 <param name="start_date" type="text" value="" label="Start date" help="Format must be yyyy-mm-dd">
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108 <validator type="expression" message="Date must have the format yyyy-mm-dd">value == datetime.strptime(value, "%Y-%m-%d").strftime('%Y-%m-%d')</validator>
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109 </param>
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110 <param name="end_date" type="text" value="" label="End date" help="Format must be yyyy-mm-dd">
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111 <validator type="expression" message="Date must have the format yyyy-mm-dd">value == datetime.strptime(value, "%Y-%m-%d").strftime('%Y-%m-%d')</validator>
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112 </param>
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113 </when>
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114 </conditional>
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112
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115 <param name="plot_generations_separately" type="select" label="Plot generations separately?">
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116 <option value="yes" selected="True">Yes</option>
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117 <option value="no">No</option>
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118 </param>
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119 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">
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120 <option value="yes" selected="true">Yes</option>
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121 <option value="no">No</option>
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122 </param>
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123 <conditional name="plot_nymph_life_stage_cond">
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124 <param name="plot_nymph_life_stage" type="select" label="Plot nymph life stage?">
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125 <option value="yes" selected="true">Yes</option>
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126 <option value="no">No</option>
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127 </param>
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128 <when value="yes">
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129 <param name="life_stages_nymph" type="select" multiple="true" label="Select nymph life stage">
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130 <option value="Total" selected="true">All</option>
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131 <option value="Young">Young</option>
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132 <option value="Old">Old</option>
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133 </param>
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134 </when>
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135 <when value="no"/>
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136 </conditional>
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137 <conditional name="plot_adult_life_stage_cond">
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138 <param name="plot_adult_life_stage" type="select" label="Plot adult life stage?">
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139 <option value="yes" selected="true">Yes</option>
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140 <option value="no">No</option>
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141 </param>
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142 <when value="yes">
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143 <param name="life_stages_adult" type="select" multiple="true" label="Select adult life stage">
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144 <option value="Total" selected="true">All</option>
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145 <option value="Pre-vittelogenic">Pre-vittelogenic</option>
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146 <option value="Vittelogenic">Vittelogenic</option>
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147 <option value="Diapausing">Diapausing</option>
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148 </param>
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149 </when>
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150 <when value="no"/>
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151 </conditional>
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152 <param name="plot_std_error" type="select" label="Plot standard error?">
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153 <option value="yes" selected="True">Yes</option>
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154 <option value="no">No</option>
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155 </param>
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156 </inputs>
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157 <outputs>
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158 <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
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159 <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/>
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160 </collection>
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161 <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
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162 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
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163 </collection>
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164 </outputs>
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165 <tests>
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166 <test>
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167 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
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168 <param name="merge_ytd_temperature_data" value="no"/>
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169 <param name="replications" value="2"/>
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170 <param name="plot_generations_separately" value="no"/>
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171 <param name="plot_egg_life_stage" value="no"/>
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172 <param name="life_stages_nymph" value="Young"/>
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173 <param name="life_stages_adult" value="Pre-vittelogenic"/>
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174 <output_collection name="output_data_collection" type="list">
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175 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
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176 </output_collection>
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177 <output_collection name="output_plots_collection" type="list">
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178 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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179 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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180 </output_collection>
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181 </test>
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182 <test>
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183 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
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184 <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/>
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185 <param name="location" value="State College PA"/>
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186 <param name="replications" value="2"/>
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187 <param name="plot_generations_separately" value="no"/>
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188 <param name="plot_egg_life_stage" value="no"/>
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189 <param name="life_stages_nymph" value="Young"/>
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190 <param name="life_stages_adult" value="Pre-vittelogenic"/>
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191 <output_collection name="output_data_collection" type="list">
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192 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
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193 </output_collection>
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194 <output_collection name="output_plots_collection" type="list">
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195 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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196 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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197 </output_collection>
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198 </test>
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199 <test>
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200 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
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201 <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/>
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202 <param name="location" value="State College PA"/>
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203 <param name="replications" value="2"/>
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204 <param name="plot_generations_separately" value="no"/>
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205 <output_collection name="output_data_collection" type="list">
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206 <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/>
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207 </output_collection>
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208 <output_collection name="output_plots_collection" type="list">
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209 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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210 <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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211 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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212 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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213 </output_collection>
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214 </test>
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215 <test>
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216 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
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217 <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/>
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218 <param name="location" value="State College PA"/>
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219 <param name="replications" value="2"/>
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220 <param name="plot_egg_life_stage" value="no"/>
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221 <param name="life_stages_nymph" value="Old"/>
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222 <param name="plot_adult_life_stage" value="no"/>
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223 <output_collection name="output_data_collection" type="list">
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224 <element name="01_generation_P.csv" file="output_p_3.csv" ftype="csv" compare="contains"/>
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225 <element name="02_generation_F1.csv" file="output_f1_3.csv" ftype="csv" compare="contains"/>
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226 <element name="03_generation_F2.csv" file="output_f2_3.csv" ftype="csv" compare="contains"/>
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227 <element name="04_combined_generations.csv" file="output_combined3.csv" ftype="csv" compare="contains"/>
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228 </output_collection>
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229 <output_collection name="output_plots_collection" type="list">
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230 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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231 </output_collection>
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232 </test>
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233 <test>
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234 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
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235 <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/>
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236 <param name="location" value="State College PA"/>
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237 <param name="replications" value="2"/>
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238 <output_collection name="output_data_collection" type="list">
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239 <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/>
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240 <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/>
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241 <element name="03_generation_F2.csv" file="output_f2_4.csv" ftype="csv" compare="contains"/>
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242 <element name="04_combined_generations.csv" file="output_combined4.csv" ftype="csv" compare="contains"/>
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243 </output_collection>
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244 <output_collection name="output_plots_collection" type="list">
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245 <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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246 <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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247 <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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248 <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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249 </output_collection>
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250 </test>
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251 </tests>
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252 <help>
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253 **What it does**
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254
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255 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
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256
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257 -----
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258
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259 **Required options**
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260
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112
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261 * **30 year normals temperature data** - the dataset from your history containing the 30-year normals temperature data (available at http://pestwatch.psu.edu/ghcn).
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262 * **Merge year-to-date temperature data with 30 year normals temperature data** - select Yes to merge a year-to-date temperature dataset from your history into the selected 30 year normals temperature data.
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263
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264 * **Year-to-date temperature data** - the dataset from your history containing the year-to-date temperature data (available at http://pestwatch.psu.edu/minmax).
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265
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266 * **Location** - the location associated with the selected temperature data.
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110
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267 * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed.
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268 * **Number of replications** - number of replications.
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108
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269 * **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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270 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
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271 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
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272 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
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273 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
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274 * **Adjustment oviposition rate** - adjustment oviposition rate.
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275 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
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276 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
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277 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
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278 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
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279 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
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112
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280 * **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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281 * **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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282 * **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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283
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284 * **Select nymph life stage** - select the nymph life stage for plotting.
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285
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286 * **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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287
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288 * **Select adult life stage** - select the adult life stage for plotting.
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289
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108
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290 * **Plot standard error** - add standard error lines to plot.
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0
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291 </help>
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292 <citations>
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293 <citation type="doi">10.3389/fphys.2016.00165</citation>
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17
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294 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
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13
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295 <citation type="doi">10.7289/V5D21VHZ</citation>
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0
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296 </citations>
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297 </tool>
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