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comparison insect_phenology_model.xml @ 112:bcb12b7e8563 draft

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author greg
date Tue, 29 May 2018 09:00:25 -0400
parents 1e28f7f61bb0
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111:37ac68b6ff10 112:bcb12b7e8563
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")
11 #set life_stages = list()
12 #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage
13 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage
14 #if str($plot_egg_life_stage) == "yes":
15 $life_stages.append("Egg")
16 #end if
17 #if str($plot_nymph_life_stage) == "yes":
18 $life_stages.append("Nymph")
19 #end if
20 #if str($plot_adult_life_stage) == "yes":
21 $life_stages.append("Adult")
22 #end if
23 #if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes":
24 $life_stages.append("Total")
25 #end if
26 #set life_stages = ",".join($life_stages)
27 mkdir output_data_dir &&
28 mkdir output_plots_dir &&
7 Rscript '$__tool_directory__/insect_phenology_model.R' 29 Rscript '$__tool_directory__/insect_phenology_model.R'
8 --adult_mortality $adult_mortality 30 --adult_mortality $adult_mortality
9 --adult_accumulation $adult_accumulation 31 --adult_accumulation $adult_accumulation
10 --egg_mortality $egg_mortality 32 --egg_mortality $egg_mortality
11 --input '$input' 33 #if str($merge_ytd_temperature_data_cond.merge_ytd_temperature_data) == "yes":
34 --input_ytd '$merge_ytd_temperature_data_cond.input_ytd'
35 --location '$merge_ytd_temperature_data_cond.location'
36 --num_days_ytd $merge_ytd_temperature_data_cond.input_ytd.metadata.data_lines
37 #end if
38 --input_norm '$input_norm'
12 --insect '$insect' 39 --insect '$insect'
13 --insects_per_replication $insects_per_replication 40 --insects_per_replication $insects_per_replication
14 --location '$location' 41 --life_stages '$life_stages'
42 #if str($plot_adult_life_stage) == "yes":
43 --life_stages_adult '$plot_adult_life_stage_cond.life_stages_adult'
44 #end if
45 #if str($plot_nymph_life_stage) == "yes":
46 --life_stages_nymph '$plot_nymph_life_stage_cond.life_stages_nymph'
47 #end if
15 --max_clutch_size $max_clutch_size 48 --max_clutch_size $max_clutch_size
16 --min_clutch_size $min_clutch_size 49 --min_clutch_size $min_clutch_size
17 --nymph_mortality $nymph_mortality 50 --nymph_mortality $nymph_mortality
18 --num_days $input.metadata.data_lines
19 --old_nymph_accumulation $old_nymph_accumulation 51 --old_nymph_accumulation $old_nymph_accumulation
20 --output '$output'
21 --oviposition $oviposition 52 --oviposition $oviposition
22 --photoperiod $photoperiod 53 --photoperiod $photoperiod
23 --replications $replications 54 --replications $replications
24 --std_error_plot $std_error_plot 55 --plot_generations_separately $plot_generations_separately
25 --young_nymph_accumulation $young_nymph_accumulation]]></command> 56 --plot_std_error $plot_std_error
57 --young_nymph_accumulation $young_nymph_accumulation
58 &>ipm_log.txt;
59 if [[ $? -ne 0 ]]; then
60 cp ipm_log.txt '$error_file';
61 exit 1;
62 fi]]></command>
26 <inputs> 63 <inputs>
27 <param name="input" type="data" format="csv" label="Temperature data" /> 64 <param name="input_norm" type="data" format="csv" label="30 year normals temperature data">
28 <param name="location" type="text" value="" optional="false" label="Location" /> 65 <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>
66 </param>
67 <conditional name="merge_ytd_temperature_data_cond">
68 <param name="merge_ytd_temperature_data" type="select" label="Merge year-to-date temperature data with 30 year normals temperature data?">
69 <option value="yes" selected="true">Yes</option>
70 <option value="no">No</option>
71 </param>
72 <when value="yes">
73 <param name="input_ytd" type="data" format="csv" label="Year-to-date temperature data">
74 <validator type="expression" message="Year-to-date temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator>
75 </param>
76 <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."/>
77 </when>
78 <when value="no"/>
79 </conditional>
29 <param name="insect" type="select" label="Select insect"> 80 <param name="insect" type="select" label="Select insect">
30 <option value="Brown Marmorated Stink Bug" selected="True">Brown Marmorated Stink Bug</option> 81 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
31 </param> 82 </param>
32 <param name="replications" type="integer" value="10" min="1" label="Number of replications" /> 83 <param name="replications" type="integer" value="10" min="2" label="Number of replications"/>
33 <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication" /> 84 <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication"/>
34 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> 85 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination"/>
35 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> 86 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality"/>
36 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> 87 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality"/>
37 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> 88 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality"/>
38 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" /> 89 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate"/>
39 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" /> 90 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size"/>
40 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" /> 91 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size"/>
41 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" /> 92 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)"/>
42 <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" /> 93 <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)"/>
43 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" /> 94 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)"/>
44 <param name="std_error_plot" type="select" label="Plot standard error?"> 95 <param name="plot_generations_separately" type="select" label="Plot generations separately?">
45 <option value="1" selected="True">Yes</option> 96 <option value="yes" selected="True">Yes</option>
46 <option value="0">No</option> 97 <option value="no">No</option>
98 </param>
99 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">
100 <option value="yes" selected="true">Yes</option>
101 <option value="no">No</option>
102 </param>
103 <conditional name="plot_nymph_life_stage_cond">
104 <param name="plot_nymph_life_stage" type="select" label="Plot nymph life stage?">
105 <option value="yes" selected="true">Yes</option>
106 <option value="no">No</option>
107 </param>
108 <when value="yes">
109 <param name="life_stages_nymph" type="select" multiple="true" label="Select nymph life stage">
110 <option value="Total" selected="true">All</option>
111 <option value="Young">Young</option>
112 <option value="Old">Old</option>
113 </param>
114 </when>
115 <when value="no"/>
116 </conditional>
117 <conditional name="plot_adult_life_stage_cond">
118 <param name="plot_adult_life_stage" type="select" label="Plot adult life stage?">
119 <option value="yes" selected="true">Yes</option>
120 <option value="no">No</option>
121 </param>
122 <when value="yes">
123 <param name="life_stages_adult" type="select" multiple="true" label="Select adult life stage">
124 <option value="Total" selected="true">All</option>
125 <option value="Pre-vittelogenic">Pre-vittelogenic</option>
126 <option value="Vittelogenic">Vittelogenic</option>
127 <option value="Diapausing">Diapausing</option>
128 </param>
129 </when>
130 <when value="no"/>
131 </conditional>
132 <param name="plot_std_error" type="select" label="Plot standard error?">
133 <option value="yes" selected="True">Yes</option>
134 <option value="no">No</option>
47 </param> 135 </param>
48 </inputs> 136 </inputs>
49 <outputs> 137 <outputs>
50 <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" /> 138 <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
139 <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/>
140 </collection>
141 <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
142 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
143 </collection>
51 </outputs> 144 </outputs>
52 <tests> 145 <tests>
53 <test> 146 <test>
54 <param name="input" value="state_college.csv" ftype="csv" /> 147 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
55 <param name="location" value="State College PA" /> 148 <param name="merge_ytd_temperature_data" value="no"/>
56 <param name="replications" value="10" /> 149 <param name="replications" value="2"/>
57 <output name="output" file="output.pdf" ftype="pdf" compare="contains" /> 150 <param name="plot_generations_separately" value="no"/>
151 <param name="plot_egg_life_stage" value="no"/>
152 <param name="life_stages_nymph" value="Young"/>
153 <param name="life_stages_adult" value="Pre-vittelogenic"/>
154 <output_collection name="output_data_collection" type="list">
155 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
156 </output_collection>
157 <output_collection name="output_plots_collection" type="list">
158 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
159 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
160 </output_collection>
161 </test>
162 <test>
163 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
164 <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/>
165 <param name="location" value="State College PA"/>
166 <param name="replications" value="2"/>
167 <param name="plot_generations_separately" value="no"/>
168 <param name="plot_egg_life_stage" value="no"/>
169 <param name="life_stages_nymph" value="Young"/>
170 <param name="life_stages_adult" value="Pre-vittelogenic"/>
171 <output_collection name="output_data_collection" type="list">
172 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
173 </output_collection>
174 <output_collection name="output_plots_collection" type="list">
175 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
176 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
177 </output_collection>
178 </test>
179 <test>
180 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
181 <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/>
182 <param name="location" value="State College PA"/>
183 <param name="replications" value="2"/>
184 <param name="plot_generations_separately" value="no"/>
185 <output_collection name="output_data_collection" type="list">
186 <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/>
187 </output_collection>
188 <output_collection name="output_plots_collection" type="list">
189 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
190 <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
191 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
192 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
193 </output_collection>
194 </test>
195 <test>
196 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
197 <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/>
198 <param name="location" value="State College PA"/>
199 <param name="replications" value="2"/>
200 <param name="plot_egg_life_stage" value="no"/>
201 <param name="life_stages_nymph" value="Old"/>
202 <param name="plot_adult_life_stage" value="no"/>
203 <output_collection name="output_data_collection" type="list">
204 <element name="01_generation_P.csv" file="output_p_3.csv" ftype="csv" compare="contains"/>
205 <element name="02_generation_F1.csv" file="output_f1_3.csv" ftype="csv" compare="contains"/>
206 <element name="03_generation_F2.csv" file="output_f2_3.csv" ftype="csv" compare="contains"/>
207 <element name="04_combined_generations.csv" file="output_combined3.csv" ftype="csv" compare="contains"/>
208 </output_collection>
209 <output_collection name="output_plots_collection" type="list">
210 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
211 </output_collection>
212 </test>
213 <test>
214 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
215 <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/>
216 <param name="location" value="State College PA"/>
217 <param name="replications" value="2"/>
218 <output_collection name="output_data_collection" type="list">
219 <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/>
220 <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/>
221 <element name="03_generation_F2.csv" file="output_f2_4.csv" ftype="csv" compare="contains"/>
222 <element name="04_combined_generations.csv" file="output_combined4.csv" ftype="csv" compare="contains"/>
223 </output_collection>
224 <output_collection name="output_plots_collection" type="list">
225 <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
226 <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
227 <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
228 <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
229 </output_collection>
58 </test> 230 </test>
59 </tests> 231 </tests>
60 <help> 232 <help>
61 **What it does** 233 **What it does**
62 234
64 236
65 ----- 237 -----
66 238
67 **Required options** 239 **Required options**
68 240
241 * **30 year normals temperature data** - the dataset from your history containing the 30-year normals temperature data (available at http://pestwatch.psu.edu/ghcn).
242 * **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.
243
244 * **Year-to-date temperature data** - the dataset from your history containing the year-to-date temperature data (available at http://pestwatch.psu.edu/minmax).
245
69 * **Location** - the location associated with the selected temperature data. 246 * **Location** - the location associated with the selected temperature data.
70 * **Temperature data** - select the dataset from your history containing the temperature data.
71 * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed. 247 * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed.
72 * **Number of replications** - number of replications. 248 * **Number of replications** - number of replications.
73 * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects. 249 * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects.
74 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination. 250 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
75 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality. 251 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
79 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size. 255 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
80 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size 256 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
81 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph). 257 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
82 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph). 258 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
83 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult). 259 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
260 * **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.
261 * **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.
262 * **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.
263
264 * **Select nymph life stage** - select the nymph life stage for plotting.
265
266 * **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.
267
268 * **Select adult life stage** - select the adult life stage for plotting.
269
84 * **Plot standard error** - add standard error lines to plot. 270 * **Plot standard error** - add standard error lines to plot.
85
86 </help> 271 </help>
87 <citations> 272 <citations>
88 <citation type="doi">10.3389/fphys.2016.00165</citation> 273 <citation type="doi">10.3389/fphys.2016.00165</citation>
89 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation> 274 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
90 <citation type="doi">10.7289/V5D21VHZ</citation> 275 <citation type="doi">10.7289/V5D21VHZ</citation>