Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.xml @ 50:927321ed0322 draft

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author greg
date Tue, 07 Aug 2018 12:59:06 -0400
parents 99e1c1300fcd
children 5bb1d76c29ca
comparison
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49:1b6864c5b50a 50:927321ed0322
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #import os 7 #import os
8 #set output_data_dir = "output_data_dir" 8 #set output_data_dir = "output_data_dir"
9 #set output_plots_dir = "output_plots_dir" 9 #set output_plots_dir = "output_plots_dir"
10 #set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv") 10 #set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv")
11 #set custom_date_interval = $custom_date_interval_cond.custom_date_interval
12 #set life_stages = list() 11 #set life_stages = list()
13 #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage 12 #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage
14 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage 13 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage
15 #if str($plot_egg_life_stage) == "yes": 14 #if str($plot_egg_life_stage) == "yes":
16 $life_stages.append("Egg") 15 $life_stages.append("Egg")
53 --oviposition $oviposition 52 --oviposition $oviposition
54 --photoperiod $photoperiod 53 --photoperiod $photoperiod
55 --plot_generations_separately $plot_generations_separately 54 --plot_generations_separately $plot_generations_separately
56 --plot_std_error $plot_std_error 55 --plot_std_error $plot_std_error
57 --replications $replications 56 --replications $replications
58 #if str($custom_date_interval) == "yes": 57 --script_dir '$__tool_directory__'
59 --start_date '$custom_date_interval_cond.start_date'
60 --end_date '$custom_date_interval_cond.end_date'
61 #end if
62 --young_nymph_accumulation $young_nymph_accumulation 58 --young_nymph_accumulation $young_nymph_accumulation
63 &>ipm_log.txt; 59 &>ipm_log.txt;
64 if [[ $? -ne 0 ]]; then 60 if [[ $? -ne 0 ]]; then
65 cp ipm_log.txt '$error_file'; 61 cp ipm_log.txt '$error_file';
66 exit 1; 62 exit 1;
95 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size"/> 91 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size"/>
96 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size"/> 92 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size"/>
97 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)"/> 93 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)"/>
98 <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)"/> 94 <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)"/>
99 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)"/> 95 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)"/>
100 <conditional name="custom_date_interval_cond">
101 <param name="custom_date_interval" type="select" label="Set date interval for plots?" help="Scales the x axis in plots from weeks to days">
102 <option value="no" selected="true">No</option>
103 <option value="yes">Yes</option>
104 </param>
105 <when value="no"/>
106 <when value="yes">
107 <param name="start_date" type="text" value="" label="Start date" help="Format must be yyyy-mm-dd">
108 <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>
109 </param>
110 <param name="end_date" type="text" value="" label="End date" help="Format must be yyyy-mm-dd">
111 <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>
112 </param>
113 </when>
114 </conditional>
115 <param name="plot_generations_separately" type="select" label="Plot generations separately?"> 96 <param name="plot_generations_separately" type="select" label="Plot generations separately?">
116 <option value="yes" selected="True">Yes</option> 97 <option value="yes" selected="True">Yes</option>
117 <option value="no">No</option> 98 <option value="no">No</option>
118 </param> 99 </param>
119 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?"> 100 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">