Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.xml @ 37:b7dcecf5476a draft

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author greg
date Tue, 10 Apr 2018 14:22:38 -0400
parents ef5add7dea47
children d8e6304dc5e4
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36:5097cfeedc4f 37:b7dcecf5476a
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 $egg_mortality
33 --input '$input' 33 --input_ytd '$input_ytd'
34 --input_norm '$input_norm'
34 --insect '$insect' 35 --insect '$insect'
35 --insects_per_replication $insects_per_replication 36 --insects_per_replication $insects_per_replication
36 --life_stages '$life_stages' 37 --life_stages '$life_stages'
37 #if str($plot_adult_life_stage) == "yes": 38 #if str($plot_adult_life_stage) == "yes":
38 --life_stages_adult '$plot_adult_life_stage_cond.life_stages_adult' 39 --life_stages_adult '$plot_adult_life_stage_cond.life_stages_adult'
42 #end if 43 #end if
43 --location '$location' 44 --location '$location'
44 --max_clutch_size $max_clutch_size 45 --max_clutch_size $max_clutch_size
45 --min_clutch_size $min_clutch_size 46 --min_clutch_size $min_clutch_size
46 --nymph_mortality $nymph_mortality 47 --nymph_mortality $nymph_mortality
47 --num_days $input.metadata.data_lines 48 --num_days_ytd $input_ytd.metadata.data_lines
48 --old_nymph_accumulation $old_nymph_accumulation 49 --old_nymph_accumulation $old_nymph_accumulation
49 --oviposition $oviposition 50 --oviposition $oviposition
50 --photoperiod $photoperiod 51 --photoperiod $photoperiod
51 --replications $replications 52 --replications $replications
52 --plot_generations_separately $plot_generations_separately 53 --plot_generations_separately $plot_generations_separately
56 if [[ $? -ne 0 ]]; then 57 if [[ $? -ne 0 ]]; then
57 cp ipm_log.txt '$error_file'; 58 cp ipm_log.txt '$error_file';
58 exit 1; 59 exit 1;
59 fi]]></command> 60 fi]]></command>
60 <inputs> 61 <inputs>
61 <param name="input" type="data" format="csv" label="Temperature data" /> 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">
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>
67 </param>
62 <param name="location" type="text" value="" optional="false" label="Location" /> 68 <param name="location" type="text" value="" optional="false" label="Location" />
63 <param name="insect" type="select" label="Select insect"> 69 <param name="insect" type="select" label="Select insect">
64 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option> 70 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
65 </param> 71 </param>
66 <param name="replications" type="integer" value="10" min="2" label="Number of replications" /> 72 <param name="replications" type="integer" value="10" min="2" label="Number of replications" />
125 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf" /> 131 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf" />
126 </collection> 132 </collection>
127 </outputs> 133 </outputs>
128 <tests> 134 <tests>
129 <test> 135 <test>
130 <param name="input" value="state_college.csv" ftype="csv" /> 136 <param name="input_ytd" value="state_college.csv" ftype="csv" />
131 <param name="location" value="State College PA" /> 137 <param name="location" value="State College PA" />
132 <param name="replications" value="2" /> 138 <param name="replications" value="2" />
133 <param name="plot_generations_separately" value="no" /> 139 <param name="plot_generations_separately" value="no" />
134 <param name="plot_egg_life_stage" value="no" /> 140 <param name="plot_egg_life_stage" value="no" />
135 <param name="life_stages_nymph" value="Young" /> 141 <param name="life_stages_nymph" value="Young" />
141 <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 147 <element name="02_young_nymph_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"/> 148 <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
143 </output_collection> 149 </output_collection>
144 </test> 150 </test>
145 <test> 151 <test>
146 <param name="input" value="state_college.csv" ftype="csv" /> 152 <param name="input_ytd" value="state_college.csv" ftype="csv" />
147 <param name="location" value="State College PA" /> 153 <param name="location" value="State College PA" />
148 <param name="replications" value="2" /> 154 <param name="replications" value="2" />
149 <param name="plot_generations_separately" value="no" /> 155 <param name="plot_generations_separately" value="no" />
150 <output_collection name="output_data_collection" type="list"> 156 <output_collection name="output_data_collection" type="list">
151 <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/> 157 <element name="04_combined_generations.csv" file="output_combined2.csv" ftype="csv" compare="contains"/>
156 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 162 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
157 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 163 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
158 </output_collection> 164 </output_collection>
159 </test> 165 </test>
160 <test> 166 <test>
161 <param name="input" value="state_college.csv" ftype="csv" /> 167 <param name="input_ytd" value="state_college.csv" ftype="csv" />
162 <param name="location" value="State College PA" /> 168 <param name="location" value="State College PA" />
163 <param name="replications" value="2" /> 169 <param name="replications" value="2" />
164 <param name="plot_egg_life_stage" value="no" /> 170 <param name="plot_egg_life_stage" value="no" />
165 <param name="life_stages_nymph" value="Old" /> 171 <param name="life_stages_nymph" value="Old" />
166 <param name="plot_adult_life_stage" value="no" /> 172 <param name="plot_adult_life_stage" value="no" />
173 <output_collection name="output_plots_collection" type="list"> 179 <output_collection name="output_plots_collection" type="list">
174 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 180 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
175 </output_collection> 181 </output_collection>
176 </test> 182 </test>
177 <test> 183 <test>
178 <param name="input" value="state_college.csv" ftype="csv" /> 184 <param name="input_ytd" value="state_college.csv" ftype="csv" />
179 <param name="location" value="State College PA" /> 185 <param name="location" value="State College PA" />
180 <param name="replications" value="2" /> 186 <param name="replications" value="2" />
181 <output_collection name="output_data_collection" type="list"> 187 <output_collection name="output_data_collection" type="list">
182 <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/> 188 <element name="01_generation_P.csv" file="output_p_4.csv" ftype="csv" compare="contains"/>
183 <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/> 189 <element name="02_generation_F1.csv" file="output_f1_4.csv" ftype="csv" compare="contains"/>