|
3
|
1 <tool id="insect_phenology_model" name="Insect phenology model" version="1.1.0">
|
|
0
|
2 <description>expressing stage-specific phenology and population dynamics</description>
|
|
|
3 <requirements>
|
|
4
|
4 <requirement type="package" version="1.4.4">r-optparse</requirement>
|
|
0
|
5 </requirements>
|
|
2
|
6 <command detect_errors="exit_code"><![CDATA[
|
|
0
|
7 Rscript '$__tool_directory__/insect_phenology_model.R'
|
|
|
8 -a $adult_mort
|
|
|
9 -b $adult_accum
|
|
|
10 -c $egg_mort
|
|
2
|
11 -e '$location'
|
|
0
|
12 -f $max_clutch_size
|
|
|
13 -i $min_clutch_size
|
|
|
14 -j $nymph_mort
|
|
|
15 -k $old_nymph_accum
|
|
3
|
16 -n $input.metadata.data_lines
|
|
2
|
17 -o '$output'
|
|
0
|
18 -p $oviposition
|
|
|
19 -q $photoperiod
|
|
|
20 -s $replications
|
|
|
21 -t $se_plot
|
|
3
|
22 -v '$input'
|
|
4
|
23 -y $young_nymph_accum]]></command>
|
|
0
|
24 <inputs>
|
|
4
|
25 <param name="input" type="data" format="csv" label="Temperature data" />
|
|
2
|
26 <param name="location" type="text" value="" optional="false" label="Location" />
|
|
0
|
27 <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
|
|
|
28 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
|
|
|
29 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
|
|
|
30 <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
|
|
|
31 <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
|
|
|
32 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
|
|
|
33 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
|
|
|
34 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
|
|
|
35 <param name="young_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (egg->young nymph)" />
|
|
|
36 <param name="old_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (young nymph->old nymph)" />
|
|
|
37 <param name="adult_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (old nymph->adult)" />
|
|
|
38 <param name="se_plot" type="select" label="Plot SE?">
|
|
|
39 <option value="1" selected="True">Yes</option>
|
|
|
40 <option value="0">No</option>
|
|
|
41 </param>
|
|
|
42 </inputs>
|
|
|
43 <outputs>
|
|
3
|
44 <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" />
|
|
0
|
45 </outputs>
|
|
|
46 <tests>
|
|
|
47 <test>
|
|
3
|
48 <param name="input" value="state_college.csv" ftype="csv" />
|
|
|
49 <param name="location" value="State College PA" />
|
|
|
50 <param name="replications" value="10" />
|
|
0
|
51 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
|
|
|
52 </test>
|
|
|
53 </tests>
|
|
|
54 <help>
|
|
|
55 **What it does**
|
|
|
56
|
|
|
57 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
|
|
|
58
|
|
|
59 -----
|
|
|
60
|
|
|
61 **Required options**
|
|
|
62
|
|
|
63 * **Location** - the location associated with the selected temperature data.
|
|
|
64 * **Temperature data** - select the dataset from your history containing the temperature data.
|
|
|
65 * **Number of replications** - number of replications.
|
|
|
66 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
|
|
|
67 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
|
|
|
68 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
|
|
|
69 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
|
|
|
70 * **Adjustment oviposition rate** - adjustment oviposition rate.
|
|
|
71 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
|
|
|
72 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
|
|
|
73 * **Adjustment of DD accumulation (egg->young nymph)** - adjustment of DD accumulation (egg->young nymph).
|
|
|
74 * **Adjustment of DD accumulation (young nymph->old nymph)** - adjustment of DD accumulation (young nymph->old nymph).
|
|
|
75 * **Adjustment of DD accumulation (old nymph->adult)** - adjustment of DD accumulation (old nymph->adult).
|
|
|
76 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
|
|
|
77
|
|
|
78 </help>
|
|
|
79 <citations>
|
|
|
80 <citation type="doi">10.3389/fphys.2016.00165</citation>
|
|
3
|
81 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
|
|
|
82 <citation type="doi">10.7289/V5D21VHZ</citation>
|
|
0
|
83 </citations>
|
|
|
84 </tool>
|
