Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.xml @ 30:0e49e1d1c5a1 draft

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author greg
date Mon, 19 Mar 2018 10:30:23 -0400
parents dd0f1b7528aa
children 94afb3e484c3
comparison
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29:dd0f1b7528aa 30:0e49e1d1c5a1
45 --photoperiod $photoperiod 45 --photoperiod $photoperiod
46 --replications $replications 46 --replications $replications
47 --plot_generations_separately $plot_generations_separately 47 --plot_generations_separately $plot_generations_separately
48 --plot_std_error $plot_std_error 48 --plot_std_error $plot_std_error
49 --young_nymph_accumulation $young_nymph_accumulation 49 --young_nymph_accumulation $young_nymph_accumulation
50 --output '$output' 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
51 &>ipm_log.txt; 56 &>ipm_log.txt;
52 if [[ $? -ne 0 ]]; then 57 if [[ $? -ne 0 ]]; then
53 cp ipm_log.txt '$output'; 58 cp ipm_log.txt '$output_combined';
54 exit 1; 59 exit 1;
55 fi]]></command> 60 fi]]></command>
56 <inputs> 61 <inputs>
57 <param name="input" type="data" format="csv" label="Temperature data" /> 62 <param name="input" type="data" format="csv" label="Temperature data" />
58 <param name="location" type="text" value="" optional="false" label="Location" /> 63 <param name="location" type="text" value="" optional="false" label="Location" />
112 <option value="yes" selected="True">Yes</option> 117 <option value="yes" selected="True">Yes</option>
113 <option value="no">No</option> 118 <option value="no">No</option>
114 </param> 119 </param>
115 </inputs> 120 </inputs>
116 <outputs> 121 <outputs>
117 <data name="output" format="csv" label="${tool.name} (analyzed data) on ${on_string}"/> 122 <data name="output_p" format="csv" label="${tool.name} (P generation) on ${on_string}">
123 <filter>plot_generations_separately == 'yes'</filter>
124 </data>
125 <data name="output_f1" format="csv" label="${tool.name} (F1 generation) on ${on_string}">
126 <filter>plot_generations_separately == 'yes'</filter>
127 </data>
128 <data name="output_f2" format="csv" label="${tool.name} (F2 generation) 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 ${on_string}"/>
118 <collection name="output_collection" type="list" label="${tool.name} (plots), on ${on_string}"> 132 <collection name="output_collection" type="list" label="${tool.name} (plots), on ${on_string}">
119 <discover_datasets pattern="__name__" directory="output_dir" format="pdf" /> 133 <discover_datasets pattern="__name__" directory="output_dir" format="pdf" />
120 </collection> 134 </collection>
121 </outputs> 135 </outputs>
122 <tests> 136 <tests>
126 <param name="replications" value="2" /> 140 <param name="replications" value="2" />
127 <param name="plot_generations_separately" value="no" /> 141 <param name="plot_generations_separately" value="no" />
128 <param name="plot_egg_life_stage" value="no" /> 142 <param name="plot_egg_life_stage" value="no" />
129 <param name="life_stages_nymph" value="Young" /> 143 <param name="life_stages_nymph" value="Young" />
130 <param name="life_stages_adult" value="Pre-vittelogenic" /> 144 <param name="life_stages_adult" value="Pre-vittelogenic" />
131 <output name="output" file="output1.csv" ftype="csv" compare="contains"/> 145 <output name="output_combined" file="output1.csv" ftype="csv" compare="contains"/>
132 <output_collection name="output_collection" type="list"> 146 <output_collection name="output_collection" type="list">
133 <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"/>
134 <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"/>
135 </output_collection> 149 </output_collection>
136 </test> 150 </test>
137 <test> 151 <test>
138 <param name="input" value="state_college.csv" ftype="csv" /> 152 <param name="input" value="state_college.csv" ftype="csv" />
139 <param name="location" value="State College PA" /> 153 <param name="location" value="State College PA" />
140 <param name="replications" value="2" /> 154 <param name="replications" value="2" />
141 <param name="plot_generations_separately" value="no" /> 155 <param name="plot_generations_separately" value="no" />
142 <output name="output" file="output2.csv" ftype="csv" compare="contains"/> 156 <output name="output_combined" file="output2.csv" ftype="csv" compare="contains"/>
143 <output_collection name="output_collection" type="list"> 157 <output_collection name="output_collection" type="list">
144 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 158 <element name="01_egg_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
145 <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 159 <element name="04_total_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
146 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 160 <element name="08_total_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
147 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 161 <element name="09_total_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
152 <param name="location" value="State College PA" /> 166 <param name="location" value="State College PA" />
153 <param name="replications" value="2" /> 167 <param name="replications" value="2" />
154 <param name="plot_egg_life_stage" value="no" /> 168 <param name="plot_egg_life_stage" value="no" />
155 <param name="life_stages_nymph" value="Old" /> 169 <param name="life_stages_nymph" value="Old" />
156 <param name="plot_adult_life_stage" value="no" /> 170 <param name="plot_adult_life_stage" value="no" />
157 <output name="output" file="output3.csv" ftype="csv" compare="contains"/> 171 <output name="output_combined" file="output3.csv" ftype="csv" compare="contains"/>
158 <output_collection name="output_collection" type="list"> 172 <output_collection name="output_collection" type="list">
159 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 173 <element name="03_old_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
160 </output_collection> 174 </output_collection>
161 </test> 175 </test>
162 <test> 176 <test>
163 <param name="input" value="state_college.csv" ftype="csv" /> 177 <param name="input" value="state_college.csv" ftype="csv" />
164 <param name="location" value="State College PA" /> 178 <param name="location" value="State College PA" />
165 <param name="replications" value="2" /> 179 <param name="replications" value="2" />
166 <output name="output" file="output4.csv" ftype="csv" compare="contains"/> 180 <output name="output_combined" file="output4.csv" ftype="csv" compare="contains"/>
167 <output_collection name="output_collection" type="list"> 181 <output_collection name="output_collection" type="list">
168 <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 182 <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
169 <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 183 <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
170 <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 184 <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
171 <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/> 185 <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>