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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="1.10.4">r-data.table</requirement>
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5 <requirement type="package" version="2.2.6">r-hash</requirement>
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6 <requirement type="package" version="1.4.4">r-optparse</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import os
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10
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10 #set input_data_dir = 'input_data_dir'
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11 #set output_data_dir = "output_data_dir"
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12 #set output_plots_dir = "output_plots_dir"
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13 #set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv")
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14 #set job = $input_data[0].creating_job
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15 #set tool_parameters = ""
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16 #for $p in $job.parameters:
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17 #set tool_parameters = $tool_parameters + "__SeP__" + $p.name
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18 #set tool_parameters = $tool_parameters + "__SeP__" + $p.value
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19 #end for
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20 mkdir $input_data_dir &&
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21 mkdir output_data_dir &&
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22 mkdir output_plots_dir &&
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23 #for $i in $input_data:
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24 #set filename = $i.file_name
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25 #set name = $i.name
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26 ln -s $filename $input_data_dir/$name &&
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27 #end for
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28 Rscript '$__tool_directory__/extract_ipm_date_interval.R'
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29 --end_date '$end_date'
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30 --input_data_dir '$input_data_dir'
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31 --script_dir '$__tool_directory__'
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32 --start_date '$start_date'
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33 --tool_parameters '$tool_parameters'
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34 &>eipmdi_log.txt;
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35 if [[ $? -ne 0 ]]; then
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36 cp eipmdi_log.txt '$error_file';
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37 exit 1;
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38 fi]]></command>
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39 <inputs>
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40 <param name="input_data" type="data_collection" format="csv" collection_type="list" label="Insect phenology model data files" />
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41 <param name="start_date" type="text" value="" label="Start date" help="Format must be yyyy-mm-dd">
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42 <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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43 </param>
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44 <param name="end_date" type="text" value="" label="End date" help="Format must be yyyy-mm-dd">
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45 <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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46 </param>
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47 </inputs>
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48 <outputs>
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49 <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
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50 <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/>
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51 </collection>
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52 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
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53 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
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54 </collection>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <!--
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59 FIXME: Here is a sort of layout for a test, but since the input collection will be uploaded, the test
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60 will fail bacused the job parameters for the inputs will not be those produced by the insect_phenology_model
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61 tool. Testing this tool will require using the workflow testing approach.
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62 <param name="input_data">
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63 <collection type="list">
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64 <element name="input_p_1.csv" value="input_p_1.csv" ftype="csv"/>
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65 <element name="input_f1_1.csv" value="input_f1_1.csv" ftype="csv"/>
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66 <element name="input_f2_1.csv" value="input_f2_1.csv" ftype="csv"/>
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67 <element name="input_combined1.csv" value="input_combined1.csv" ftype="csv"/>
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68 </collection>
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69 </param>
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70 <param name="start_date" value="2017-04-01"/>
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71 <param name="end_date" value="2017-04-15"/>
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72 <output_collection name="output_data_collection" type="list">
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73 <element name="01_generation_P.csv" file="output_p_1.csv" ftype="csv" compare="contains"/>
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74 <element name="02_generation_F1.csv" file="output_f1_1.csv" ftype="csv" compare="contains"/>
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75 <element name="03_generation_F2.csv" file="output_f2_1.csv" ftype="csv" compare="contains"/>
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76 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
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77 </output_collection>
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78 <output_collection name="output_plot_collection" type="list">
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79 <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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80 <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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81 <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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82 <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
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83 </output_collection>
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84 -->
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85 </test>
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86 </tests>
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87 <help>
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88 **What it does**
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89
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90 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
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91
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92 -----
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93
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94 **Required options**
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95
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96 * **Plot standard error** - add standard error lines to plot.
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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 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
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101 <citation type="doi">10.7289/V5D21VHZ</citation>
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102 </citations>
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103 </tool>
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