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comparison insect_phenology_model.xml @ 33:ef5add7dea47 draft

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author greg
date Mon, 19 Mar 2018 14:48:57 -0400
parents 94afb3e484c3
children b7dcecf5476a
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32:94afb3e484c3 33:ef5add7dea47
2 <description>expressing stage-specific phenology and population dynamics</description> 2 <description>expressing stage-specific phenology and population dynamics</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4.4">r-optparse</requirement> 4 <requirement type="package" version="1.4.4">r-optparse</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #import os
8 #set output_data_dir = "output_data_dir"
9 #set output_plots_dir = "output_plots_dir"
10 #set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv")
7 #set life_stages = list() 11 #set life_stages = list()
8 #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
9 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage 13 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage
10 #if str($plot_egg_life_stage) == "yes": 14 #if str($plot_egg_life_stage) == "yes":
11 $life_stages.append("Egg") 15 $life_stages.append("Egg")
18 #end if 22 #end if
19 #if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes": 23 #if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes":
20 $life_stages.append("Total") 24 $life_stages.append("Total")
21 #end if 25 #end if
22 #set life_stages = ",".join($life_stages) 26 #set life_stages = ",".join($life_stages)
23 mkdir output_dir && 27 mkdir output_data_dir &&
28 mkdir output_plots_dir &&
24 Rscript '$__tool_directory__/insect_phenology_model.R' 29 Rscript '$__tool_directory__/insect_phenology_model.R'
25 --adult_mortality $adult_mortality 30 --adult_mortality $adult_mortality
26 --adult_accumulation $adult_accumulation 31 --adult_accumulation $adult_accumulation
27 --egg_mortality $egg_mortality 32 --egg_mortality $egg_mortality
28 --input '$input' 33 --input '$input'
45 --photoperiod $photoperiod 50 --photoperiod $photoperiod
46 --replications $replications 51 --replications $replications
47 --plot_generations_separately $plot_generations_separately 52 --plot_generations_separately $plot_generations_separately
48 --plot_std_error $plot_std_error 53 --plot_std_error $plot_std_error
49 --young_nymph_accumulation $young_nymph_accumulation 54 --young_nymph_accumulation $young_nymph_accumulation
50 --output_combined '$output_combined'
51 #if str($plot_generations_separately) == "yes":
52 --output_p '$output_p'
53 --output_f1 '$output_f1'
54 --output_f2 '$output_f2'
55 #end if
56 &>ipm_log.txt; 55 &>ipm_log.txt;
57 if [[ $? -ne 0 ]]; then 56 if [[ $? -ne 0 ]]; then
58 cp ipm_log.txt '$output_combined'; 57 cp ipm_log.txt '$error_file';
59 exit 1; 58 exit 1;
60 fi]]></command> 59 fi]]></command>
61 <inputs> 60 <inputs>
62 <param name="input" type="data" format="csv" label="Temperature data" /> 61 <param name="input" type="data" format="csv" label="Temperature data" />
63 <param name="location" type="text" value="" optional="false" label="Location" /> 62 <param name="location" type="text" value="" optional="false" label="Location" />
117 <option value="yes" selected="True">Yes</option> 116 <option value="yes" selected="True">Yes</option>
118 <option value="no">No</option> 117 <option value="no">No</option>
119 </param> 118 </param>
120 </inputs> 119 </inputs>
121 <outputs> 120 <outputs>
122 <data name="output_p" format="csv" label="${tool.name} (P) on ${on_string}"> 121 <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
123 <filter>plot_generations_separately == 'yes'</filter> 122 <discover_datasets pattern="__name__" directory="output_data_dir" format="csv" />
124 </data> 123 </collection>
125 <data name="output_f1" format="csv" label="${tool.name} (F1) on ${on_string}"> 124 <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
126 <filter>plot_generations_separately == 'yes'</filter> 125 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf" />
127 </data>
128 <data name="output_f2" format="csv" label="${tool.name} (F2) on ${on_string}">
129 <filter>plot_generations_separately == 'yes'</filter>
130 </data>
131 <data name="output_combined" format="csv" label="${tool.name} (combined generations) on ${on_string}"/>
132 <collection name="output_collection" type="list" label="${tool.name} (plots), on ${on_string}">
133 <discover_datasets pattern="__name__" directory="output_dir" format="pdf" />
134 </collection> 126 </collection>
135 </outputs> 127 </outputs>
136 <tests> 128 <tests>
137 <test> 129 <test>
138 <param name="input" value="state_college.csv" ftype="csv" /> 130 <param name="input" value="state_college.csv" ftype="csv" />
140 <param name="replications" value="2" /> 132 <param name="replications" value="2" />
141 <param name="plot_generations_separately" value="no" /> 133 <param name="plot_generations_separately" value="no" />
142 <param name="plot_egg_life_stage" value="no" /> 134 <param name="plot_egg_life_stage" value="no" />
143 <param name="life_stages_nymph" value="Young" /> 135 <param name="life_stages_nymph" value="Young" />
144 <param name="life_stages_adult" value="Pre-vittelogenic" /> 136 <param name="life_stages_adult" value="Pre-vittelogenic" />
145 <output name="output_combined" file="output_combined1.csv" ftype="csv" compare="contains"/> 137 <output_collection name="output_data_collection" type="list">
146 <output_collection name="output_collection" type="list"> 138 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
139 </output_collection>
140 <output_collection name="output_plots_collection" type="list">
147 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 141 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
148 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 142 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
149 </output_collection> 143 </output_collection>
150 </test> 144 </test>
151 <test> 145 <test>
152 <param name="input" value="state_college.csv" ftype="csv" /> 146 <param name="input" value="state_college.csv" ftype="csv" />
153 <param name="location" value="State College PA" /> 147 <param name="location" value="State College PA" />
154 <param name="replications" value="2" /> 148 <param name="replications" value="2" />
155 <param name="plot_generations_separately" value="no" /> 149 <param name="plot_generations_separately" value="no" />
156 <output name="output_combined" file="output_combined2.csv" ftype="csv" compare="contains"/> 150 <output_collection name="output_data_collection" type="list">
157 <output_collection name="output_collection" type="list"> 151 <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/>
152 </output_collection>
153 <output_collection name="output_plots_collection" type="list">
158 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 154 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
159 <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 155 <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
160 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 156 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
161 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 157 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
162 </output_collection> 158 </output_collection>
166 <param name="location" value="State College PA" /> 162 <param name="location" value="State College PA" />
167 <param name="replications" value="2" /> 163 <param name="replications" value="2" />
168 <param name="plot_egg_life_stage" value="no" /> 164 <param name="plot_egg_life_stage" value="no" />
169 <param name="life_stages_nymph" value="Old" /> 165 <param name="life_stages_nymph" value="Old" />
170 <param name="plot_adult_life_stage" value="no" /> 166 <param name="plot_adult_life_stage" value="no" />
171 <output name="output_p" file="output_p_3.csv" ftype="csv" compare="contains"/> 167 <output_collection name="output_data_collection" type="list">
172 <output name="output_f1" file="output_f1_3.csv" ftype="csv" compare="contains"/> 168 <element name="01_generation_P.csv" file="output_p_3.csv" ftype="csv" compare="contains"/>
173 <output name="output_f2" file="output_f2_3.csv" ftype="csv" compare="contains"/> 169 <element name="02_generation_F1.csv" file="output_f1_3.csv" ftype="csv" compare="contains"/>
174 <output name="output_combined" file="output_combined3.csv" ftype="csv" compare="contains"/> 170 <element name="03_generation_F2.csv" file="output_f2_3.csv" ftype="csv" compare="contains"/>
175 <output_collection name="output_collection" type="list"> 171 <element name="04_combined_generations.csv" file="output_combined3.csv" ftype="csv" compare="contains"/>
172 </output_collection>
173 <output_collection name="output_plots_collection" type="list">
176 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 174 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
177 </output_collection> 175 </output_collection>
178 </test> 176 </test>
179 <test> 177 <test>
180 <param name="input" value="state_college.csv" ftype="csv" /> 178 <param name="input" value="state_college.csv" ftype="csv" />
181 <param name="location" value="State College PA" /> 179 <param name="location" value="State College PA" />
182 <param name="replications" value="2" /> 180 <param name="replications" value="2" />
183 <output name="output_p" file="output_p_4.csv" ftype="csv" compare="contains"/> 181 <output_collection name="output_data_collection" type="list">
184 <output name="output_f1" file="output_f1_4.csv" ftype="csv" compare="contains"/> 182 <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/>
185 <output name="output_f2" file="output_f2_4.csv" ftype="csv" compare="contains"/> 183 <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/>
186 <output name="output_combined" file="output_combined4.csv" ftype="csv" compare="contains"/> 184 <element name="03_generation_F2.csv" file="output_f2_4.csv" ftype="csv" compare="contains"/>
187 <output_collection name="output_collection" type="list"> 185 <element name="04_combined_generations.csv" file="output_combined4.csv" ftype="csv" compare="contains"/>
186 </output_collection>
187 <output_collection name="output_plots_collection" type="list">
188 <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 188 <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
189 <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 189 <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
190 <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 190 <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
191 <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 191 <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
192 </output_collection> 192 </output_collection>