Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.xml @ 13:80d38a26b2e8 draft

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author greg
date Thu, 28 Sep 2017 10:45:53 -0400
parents e82ea5f1a179
children 4e83be4e8e97
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12:e82ea5f1a179 13:80d38a26b2e8
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$__tool_directory__/insect_phenology_model.R' 8 Rscript '$__tool_directory__/insect_phenology_model.R'
9 -a $adult_mort 9 -a $adult_mort
10 -b $adult_accum 10 -b $adult_accum
11 -c $egg_mort 11 -c $egg_mort
12 -d $latitude 12 -d $location.fields.latitude
13 -e '$location' 13 -e '$location.fields.name'
14 -f $max_clutch_size 14 -f $max_clutch_size
15 -i $min_clutch_size 15 -i $min_clutch_size
16 -j $nymph_mort 16 -j $nymph_mort
17 -k $old_nymph_accum 17 -k $old_nymph_accum
18 -n $temperature_data.metadata.data_lines
18 -o '$output' 19 -o '$output'
19 -p $oviposition 20 -p $oviposition
20 -q $photoperiod 21 -q $photoperiod
21 -s $replications 22 -s $replications
22 -t $se_plot 23 -t $se_plot
23 -u $year 24 -u $year
24 -v '$temperature_data' 25 -v '$temperature_data'
25 -y $young_nymph_accum 26 -y $young_nymph_accum
26 ]]></command> 27 ]]></command>
27 <inputs> 28 <inputs>
28 <param name="location" type="text" value="" optional="false" label="Location" /> 29 <param name="location" type="select" label="Global Historical Climatology Network Station">
29 <param name="latitude" type="float" value="0.0" label="Latitude of selected location" /> 30 <options from_file="ghcnd_stations.txt">
31 <column name="name" index="4"/>
32 <column name="station" index="0"/>
33 <column name="latitude" index="1"/>
34 </options>
35 </param>
30 <param name="temperature_data" type="data" format="csv" label="Temperature data" /> 36 <param name="temperature_data" type="data" format="csv" label="Temperature data" />
31 <param name="year" type="integer" value="2017" min="1995" label="Temperature data year" /> 37 <param name="year" type="integer" value="2017" min="1995" label="Temperature data year" />
32 <param name="replications" type="integer" value="10" min="1" label="Number of replications" /> 38 <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
33 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> 39 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
34 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> 40 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
44 <option value="1" selected="True">Yes</option> 50 <option value="1" selected="True">Yes</option>
45 <option value="0">No</option> 51 <option value="0">No</option>
46 </param> 52 </param>
47 </inputs> 53 </inputs>
48 <outputs> 54 <outputs>
49 <data name="output" format="pdf" label="${tool.name} ${location}, ${year} lat:${latitude} on ${on_string}" /> 55 <data name="output" format="pdf" label="${tool.name} ${location}, ${year} on ${on_string}" />
50 </outputs> 56 </outputs>
51 <tests> 57 <tests>
52 <test> 58 <test>
53 <param name="temperature_data" value="asheville2014.csv" ftype="csv" /> 59 <param name="temperature_data" value="asheville2014.csv" ftype="csv" />
54 <param name="location" value="asheville:35.58" /> 60 <param name="location" value="asheville:35.58" />
83 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults. 89 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
84 90
85 </help> 91 </help>
86 <citations> 92 <citations>
87 <citation type="doi">10.3389/fphys.2016.00165</citation> 93 <citation type="doi">10.3389/fphys.2016.00165</citation>
94 <citation type="doi">10.1175/JTECH-D-11-00103.22</citation>
95 <citation type="doi">10.7289/V5D21VHZ</citation>
88 </citations> 96 </citations>
89 </tool> 97 </tool>