Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.xml @ 42:64132300c62e draft

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author greg
date Mon, 23 Apr 2018 09:48:58 -0400
parents d8e6304dc5e4
children c61d3d9d44db
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41:f4d683709b7f 42:64132300c62e
28 mkdir output_plots_dir && 28 mkdir output_plots_dir &&
29 Rscript '$__tool_directory__/insect_phenology_model.R' 29 Rscript '$__tool_directory__/insect_phenology_model.R'
30 --adult_mortality $adult_mortality 30 --adult_mortality $adult_mortality
31 --adult_accumulation $adult_accumulation 31 --adult_accumulation $adult_accumulation
32 --egg_mortality $egg_mortality 32 --egg_mortality $egg_mortality
33 --input_ytd '$input_ytd' 33 #if str($merge_ytd_temperature_data_cond.merge_ytd_temperature_data) == "yes":
34 --input_ytd '$merge_ytd_temperature_data_cond.input_ytd'
35 --num_days_ytd $input_ytd.metadata.data_lines
36 #end if
34 --input_norm '$input_norm' 37 --input_norm '$input_norm'
35 --insect '$insect' 38 --insect '$insect'
36 --insects_per_replication $insects_per_replication 39 --insects_per_replication $insects_per_replication
37 --life_stages '$life_stages' 40 --life_stages '$life_stages'
38 #if str($plot_adult_life_stage) == "yes": 41 #if str($plot_adult_life_stage) == "yes":
43 #end if 46 #end if
44 --location '$location' 47 --location '$location'
45 --max_clutch_size $max_clutch_size 48 --max_clutch_size $max_clutch_size
46 --min_clutch_size $min_clutch_size 49 --min_clutch_size $min_clutch_size
47 --nymph_mortality $nymph_mortality 50 --nymph_mortality $nymph_mortality
48 --num_days_ytd $input_ytd.metadata.data_lines
49 --old_nymph_accumulation $old_nymph_accumulation 51 --old_nymph_accumulation $old_nymph_accumulation
50 --oviposition $oviposition 52 --oviposition $oviposition
51 --photoperiod $photoperiod 53 --photoperiod $photoperiod
52 --replications $replications 54 --replications $replications
53 --plot_generations_separately $plot_generations_separately 55 --plot_generations_separately $plot_generations_separately
57 if [[ $? -ne 0 ]]; then 59 if [[ $? -ne 0 ]]; then
58 cp ipm_log.txt '$error_file'; 60 cp ipm_log.txt '$error_file';
59 exit 1; 61 exit 1;
60 fi]]></command> 62 fi]]></command>
61 <inputs> 63 <inputs>
62 <param name="input_ytd" type="data" format="csv" label="Year-to-date temperature data">
63 <validator type="expression" message="Year-to-date temperature data must have 6 columns">value is not None and value.metadata.columns==6</validator>
64 </param>
65 <param name="input_norm" type="data" format="csv" label="30 year normals temperature data"> 64 <param name="input_norm" type="data" format="csv" label="30 year normals temperature data">
66 <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> 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>
67 </param> 66 </param>
68 <param name="location" type="text" value="" optional="false" label="Location" /> 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 </when>
77 <when value="no"/>
78 </conditional>
79 <param name="location" type="text" value="" optional="false" label="Location"/>
69 <param name="insect" type="select" label="Select insect"> 80 <param name="insect" type="select" label="Select insect">
70 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option> 81 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
71 </param> 82 </param>
72 <param name="replications" type="integer" value="10" min="2" label="Number of replications" /> 83 <param name="replications" type="integer" value="10" min="2" label="Number of replications"/>
73 <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"/>
74 <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"/>
75 <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"/>
76 <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"/>
77 <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"/>
78 <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"/>
79 <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"/>
80 <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"/>
81 <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)"/>
82 <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)"/>
83 <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)"/>
84 <param name="plot_generations_separately" type="select" label="Plot generations separately?"> 95 <param name="plot_generations_separately" type="select" label="Plot generations separately?">
85 <option value="yes" selected="True">Yes</option> 96 <option value="yes" selected="True">Yes</option>
86 <option value="no">No</option> 97 <option value="no">No</option>
87 </param> 98 </param>
88 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?"> 99 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">
123 <option value="no">No</option> 134 <option value="no">No</option>
124 </param> 135 </param>
125 </inputs> 136 </inputs>
126 <outputs> 137 <outputs>
127 <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}"> 138 <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
128 <discover_datasets pattern="__name__" directory="output_data_dir" format="csv" /> 139 <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/>
129 </collection> 140 </collection>
130 <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}"> 141 <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
131 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf" /> 142 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
132 </collection> 143 </collection>
133 </outputs> 144 </outputs>
134 <tests> 145 <tests>
135 <test> 146 <test>
136 <param name="input_ytd" value="state_college_partial.csv" ftype="csv" /> 147 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
137 <param name="input_norm" value="30_year_normals.csv" ftype="csv" /> 148 <param name="merge_ytd_temperature_data" value="no"/>
138 <param name="location" value="State College PA" /> 149 <param name="location" value="State College PA"/>
139 <param name="replications" value="2" /> 150 <param name="replications" value="2"/>
140 <param name="plot_generations_separately" value="no" /> 151 <param name="plot_generations_separately" value="no"/>
141 <param name="plot_egg_life_stage" value="no" /> 152 <param name="plot_egg_life_stage" value="no"/>
142 <param name="life_stages_nymph" value="Young" /> 153 <param name="life_stages_nymph" value="Young"/>
143 <param name="life_stages_adult" value="Pre-vittelogenic" /> 154 <param name="life_stages_adult" value="Pre-vittelogenic"/>
144 <output_collection name="output_data_collection" type="list"> 155 <output_collection name="output_data_collection" type="list">
145 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/> 156 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
146 </output_collection> 157 </output_collection>
147 <output_collection name="output_plots_collection" type="list"> 158 <output_collection name="output_plots_collection" type="list">
148 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 159 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
149 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 160 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
150 </output_collection> 161 </output_collection>
151 </test> 162 </test>
152 <test> 163 <test>
153 <param name="input_ytd" value="state_college_ytd.csv" ftype="csv" /> 164 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
154 <param name="input_norm" value="30_year_normals.csv" ftype="csv" /> 165 <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/>
155 <param name="location" value="State College PA" /> 166 <param name="location" value="State College PA"/>
156 <param name="replications" value="2" /> 167 <param name="replications" value="2"/>
157 <param name="plot_generations_separately" value="no" /> 168 <param name="plot_generations_separately" value="no"/>
169 <param name="plot_egg_life_stage" value="no"/>
170 <param name="life_stages_nymph" value="Young"/>
171 <param name="life_stages_adult" value="Pre-vittelogenic"/>
172 <output_collection name="output_data_collection" type="list">
173 <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
174 </output_collection>
175 <output_collection name="output_plots_collection" type="list">
176 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
177 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
178 </output_collection>
179 </test>
180 <test>
181 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
182 <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/>
183 <param name="location" value="State College PA"/>
184 <param name="replications" value="2"/>
185 <param name="plot_generations_separately" value="no"/>
158 <output_collection name="output_data_collection" type="list"> 186 <output_collection name="output_data_collection" type="list">
159 <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/> 187 <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/>
160 </output_collection> 188 </output_collection>
161 <output_collection name="output_plots_collection" type="list"> 189 <output_collection name="output_plots_collection" type="list">
162 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 190 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
164 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 192 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
165 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 193 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
166 </output_collection> 194 </output_collection>
167 </test> 195 </test>
168 <test> 196 <test>
169 <param name="input_ytd" value="state_college_partial.csv" ftype="csv" /> 197 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
170 <param name="input_norm" value="30_year_normals.csv" ftype="csv" /> 198 <param name="input_ytd" value="state_college_partial.csv" ftype="csv"/>
171 <param name="location" value="State College PA" /> 199 <param name="location" value="State College PA"/>
172 <param name="replications" value="2" /> 200 <param name="replications" value="2"/>
173 <param name="plot_egg_life_stage" value="no" /> 201 <param name="plot_egg_life_stage" value="no"/>
174 <param name="life_stages_nymph" value="Old" /> 202 <param name="life_stages_nymph" value="Old"/>
175 <param name="plot_adult_life_stage" value="no" /> 203 <param name="plot_adult_life_stage" value="no"/>
176 <output_collection name="output_data_collection" type="list"> 204 <output_collection name="output_data_collection" type="list">
177 <element name="01_generation_P.csv" file="output_p_3.csv" ftype="csv" compare="contains"/> 205 <element name="01_generation_P.csv" file="output_p_3.csv" ftype="csv" compare="contains"/>
178 <element name="02_generation_F1.csv" file="output_f1_3.csv" ftype="csv" compare="contains"/> 206 <element name="02_generation_F1.csv" file="output_f1_3.csv" ftype="csv" compare="contains"/>
179 <element name="03_generation_F2.csv" file="output_f2_3.csv" ftype="csv" compare="contains"/> 207 <element name="03_generation_F2.csv" file="output_f2_3.csv" ftype="csv" compare="contains"/>
180 <element name="04_combined_generations.csv" file="output_combined3.csv" ftype="csv" compare="contains"/> 208 <element name="04_combined_generations.csv" file="output_combined3.csv" ftype="csv" compare="contains"/>
182 <output_collection name="output_plots_collection" type="list"> 210 <output_collection name="output_plots_collection" type="list">
183 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 211 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
184 </output_collection> 212 </output_collection>
185 </test> 213 </test>
186 <test> 214 <test>
187 <param name="input_ytd" value="state_college_ytd.csv" ftype="csv" /> 215 <param name="input_norm" value="30_year_normals.csv" ftype="csv"/>
188 <param name="input_norm" value="30_year_normals.csv" ftype="csv" /> 216 <param name="input_ytd" value="state_college_ytd.csv" ftype="csv"/>
189 <param name="location" value="State College PA" /> 217 <param name="location" value="State College PA"/>
190 <param name="replications" value="2" /> 218 <param name="replications" value="2"/>
191 <output_collection name="output_data_collection" type="list"> 219 <output_collection name="output_data_collection" type="list">
192 <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/> 220 <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/>
193 <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/> 221 <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/>
194 <element name="03_generation_F2.csv" file="output_f2_4.csv" ftype="csv" compare="contains"/> 222 <element name="03_generation_F2.csv" file="output_f2_4.csv" ftype="csv" compare="contains"/>
195 <element name="04_combined_generations.csv" file="output_combined4.csv" ftype="csv" compare="contains"/> 223 <element name="04_combined_generations.csv" file="output_combined4.csv" ftype="csv" compare="contains"/>
209 237
210 ----- 238 -----
211 239
212 **Required options** 240 **Required options**
213 241
242 * **30 year normals temperature data** - the dataset from your history containing the 30-year normals temperature data (available at http://pestwatch.psu.edu/ghcn).
243 * **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.
244
245 * **Year-to-date temperature data** - the dataset from your history containing the year-to-date temperature data (available at http://pestwatch.psu.edu/minmax).
246
214 * **Location** - the location associated with the selected temperature data. 247 * **Location** - the location associated with the selected temperature data.
215 * **Temperature data** - select the dataset from your history containing the temperature data.
216 * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed. 248 * **Select insect** - currently only the Brown Marmorated Stink Bug can be analyzed.
217 * **Number of replications** - number of replications. 249 * **Number of replications** - number of replications.
218 * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects. 250 * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects.
219 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination. 251 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
220 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality. 252 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.