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comparison insect_phenology_model.xml @ 0:244c373f2a34 draft

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date Tue, 08 Aug 2017 13:14:39 -0400
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1 <?xml version="."?>
2 <tool id="insect_phenology_model" name="Insect phenology model" version="1.0.0">
3 <description>expressing stage-specific phenology and population dynamics</description>
4 <requirements>
5 <requirement type="package" version="1.3.0">r-optparse</requirement>
6 </requirements>
7 <command><![CDATA[
8 #set loc_lat_items = str($location).split(':')
9 #set loc = $loc_lat_items[0]
10 #set lat = $loc_lat_items[1]
11 Rscript '$__tool_directory__/insect_phenology_model.R'
12 -a $adult_mort
13 -b $adult_accum
14 -c $egg_mort
15 -d $lat
16 -e $loc
17 -f $max_clutch_size
18 -i $min_clutch_size
19 -j $nymph_mort
20 -k $old_nymph_accum
21 -o $output
22 -p $oviposition
23 -q $photoperiod
24 -s $replications
25 -t $se_plot
26 -u $year
27 -v '$temperature_data'
28 -y $young_nymph_accum
29 ]]></command>
30 <inputs>
31 <param name="location" type="select" label="Location">
32 <options from_file="locations.txt">
33 <column name="name" index="0"/>
34 <column name="value" index="1"/>
35 </options>
36 </param>
37 <param name="temperature_data" type="data" format="csv" label="Temperature data" />
38 <param name="year" type="select" label="Temperature data year">
39 <options from_file="years.txt">
40 <column name="name" index="0"/>
41 <column name="value" index="1"/>
42 </options>
43 </param>
44 <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
45 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
46 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
47 <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
48 <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
49 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
50 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
51 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
52 <param name="young_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (egg->young nymph)" />
53 <param name="old_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (young nymph->old nymph)" />
54 <param name="adult_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (old nymph->adult)" />
55 <param name="se_plot" type="select" label="Plot SE?">
56 <option value="1" selected="True">Yes</option>
57 <option value="0">No</option>
58 </param>
59 </inputs>
60 <outputs>
61 <data name="output" format="pdf" label="${tool.name} ${str($location).split(':')[0]}, ${year} on ${on_string}" />
62 </outputs>
63 <tests>
64 <test>
65 <param name="temperature_data" value="asheville2014.csv" ftype="csv" />
66 <param name="location" value="asheville:35.58" />
67 <param name="year" value="2014" />
68 <param name="replications" value="3" />
69 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
70 </test>
71 </tests>
72 <help>
73 **What it does**
74
75 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
76
77 -----
78
79 **Required options**
80
81 * **Location** - the location associated with the selected temperature data.
82 * **Temperature data** - select the dataset from your history containing the temperature data.
83 * **Temperature data year** - the year during which the temperature data was recorded.
84 * **Number of replications** - number of replications.
85 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
86 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
87 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
88 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
89 * **Adjustment oviposition rate** - adjustment oviposition rate.
90 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
91 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
92 * **Adjustment of DD accumulation (egg->young nymph)** - adjustment of DD accumulation (egg->young nymph).
93 * **Adjustment of DD accumulation (young nymph->old nymph)** - adjustment of DD accumulation (young nymph->old nymph).
94 * **Adjustment of DD accumulation (old nymph->adult)** - adjustment of DD accumulation (old nymph->adult).
95 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
96
97 </help>
98 <citations>
99 <citation type="doi">10.3389/fphys.2016.00165</citation>
100 </citations>
101 </tool>