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1 <tool id="ipm_date_interval" name="Extract date interval" version="1.1.0">
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2 <description>from insect phenology model data</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 <requirement type="package" version="1.10.4">r-data.table</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import os
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9 #set input_dir = 'input_dir'
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10 #set output_data_dir = "output_data_dir"
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11 #set output_plots_dir = "output_plots_dir"
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12 #set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv")
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13 mkdir $input_dir &&
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14 mkdir output_data_dir &&
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15 mkdir output_plots_dir &&
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16 #for $i in $input:
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17 #set filename = $i.file_name
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18 #set name = $i.name
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19 ln -s $filename $input_dir/$name &&
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20 #end for
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21 Rscript '$__tool_directory__/extract_ipm_date_interval.R'
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22 --end_date '$end_date'
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23 --input_dir '$input_dir'
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24 --plot_std_error $plot_std_error
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25 --script_dir '$__tool_directory__'
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26 --start_date '$start_date'
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27 &>ipm_log.txt;
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28 if [[ $? -ne 0 ]]; then
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29 cp ipm_log.txt '$error_file';
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30 exit 1;
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31 fi]]></command>
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32 <inputs>
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33 <param name="input" type="data_collection" format="csv" collection_type="list" label="Insect phenology model data files" />
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34 <param name="start_date" type="text" value="" label="Start date" help="Format must be yyyy-mm-dd">
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35 <validator type="expression" message="Date must have the format yyyy-mm-dd">len(value.split('-')[0])==4 and int(value.split('-')[0]) and len(value.split('-')[1])==2 and int(value.split('-')[1]) and len(value.split('-')[2])==2 and int(value.split('-')[2])</validator>
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36 </param>
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37 <param name="end_date" type="text" value="" label="End date" help="Format must be yyyy-mm-dd">
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38 <validator type="expression" message="Date must have the format yyyy-mm-dd">len(value.split('-')[0])==4 and int(value.split('-')[0]) and len(value.split('-')[1])==2 and int(value.split('-')[1]) and len(value.split('-')[2])==2 and int(value.split('-')[2])</validator>
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39 </param>
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40 <param name="plot_std_error" type="select" label="Plot standard error?">
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41 <option value="yes" selected="True">Yes</option>
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42 <option value="no">No</option>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
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47 <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/>
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48 </collection>
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49 <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
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50 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
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51 </collection>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input">
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56 <collection type="list">
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57 <element name="04_combined_generations.csv"/>
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58 </collection>
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59 </param>
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60 <param name="start_date" value="2017-04-01"/>
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61 <param name="end_date" value="2017-04-15"/>
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62 <output_collection name="output_data_collection" type="list">
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63 <element name="04_combined_generations.csv" file="output_combined6.csv" ftype="csv" compare="contains"/>
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64 </output_collection>
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65 <!--
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66 <output_collection name="output_plots_collection" type="list">
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67 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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68 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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69 </output_collection>
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70 -->
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71 </test>
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72 <test>
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73 <param name="input">
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74 <collection type="list">
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75 <element name="04_combined_generations.csv"/>
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76 </collection>
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77 </param>
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78 <param name="start_date" value="2017-01-01"/>
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79 <param name="end_date" value="2017-01-15"/>
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80 <output_collection name="output_data_collection" type="list">
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81 <element name="04_combined_generations.csv" file="output_combined7.csv" ftype="csv" compare="contains"/>
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82 </output_collection>
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83 <!--
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84 <output_collection name="output_plots_collection" type="list">
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85 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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86 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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87 </output_collection>
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88 -->
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89 </test>
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90 </tests>
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91 <help>
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92 **What it does**
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93
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94 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
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95
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96 -----
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97
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98 **Required options**
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99
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100 * **Plot standard error** - add standard error lines to plot.
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101 </help>
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102 <citations>
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103 <citation type="doi">10.3389/fphys.2016.00165</citation>
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104 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
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105 <citation type="doi">10.7289/V5D21VHZ</citation>
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106 </citations>
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107 </tool>
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