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comparison insect_phenology_model.xml @ 9:d9371485aaf5 draft

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author greg
date Tue, 27 Feb 2018 13:31:49 -0500
parents ad26f07a7dd8
children bd5e35775e20
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8:37f1ad91a949 9:d9371485aaf5
2 <description>expressing stage-specific phenology and population dynamics</description> 2 <description>expressing stage-specific phenology and population dynamics</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4.4">r-optparse</requirement> 4 <requirement type="package" version="1.4.4">r-optparse</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #set stages = list()
8 #set life_stages_adult = "None"
9 #set life_stage_nymph = "None"
10 #set life_stages = $life_stages_cond.life_stages
11 #for life_stage in str($life_stages).split(","):
12 #if $life_stage == "Adult":
13 #set life_stages_adult = $life_stages_cond.life_stages_adult
14 #else if $life_stage == "Nymph":
15 #set life_stage_nymph = $life_stages_cond.life_stage_nymph
16 #end if
17 $stages.append($life_stage)
18 #end for
19 #set stages = ",".join($stages)
20 mkdir output_dir &&
7 Rscript '$__tool_directory__/insect_phenology_model.R' 21 Rscript '$__tool_directory__/insect_phenology_model.R'
8 --adult_mortality $adult_mortality 22 --adult_mortality $adult_mortality
9 --adult_accumulation $adult_accumulation 23 --adult_accumulation $adult_accumulation
10 --egg_mortality $egg_mortality 24 --egg_mortality $egg_mortality
11 --input '$input' 25 --input '$input'
12 --insect '$insect' 26 --insect '$insect'
13 --insects_per_replication $insects_per_replication 27 --insects_per_replication $insects_per_replication
28 --life_stages '$stages'
29 #if str($life_stages_adult) != "None":
30 --life_stages_adult $life_stages_adult
31 #end if
32 #if str($life_stage_nymph) != "None":
33 --life_stage_nymph $life_stage_nymph
34 #end if
14 --location '$location' 35 --location '$location'
15 --max_clutch_size $max_clutch_size 36 --max_clutch_size $max_clutch_size
16 --min_clutch_size $min_clutch_size 37 --min_clutch_size $min_clutch_size
17 --nymph_mortality $nymph_mortality 38 --nymph_mortality $nymph_mortality
18 --num_days $input.metadata.data_lines 39 --num_days $input.metadata.data_lines
19 --old_nymph_accumulation $old_nymph_accumulation 40 --old_nymph_accumulation $old_nymph_accumulation
20 --output '$output'
21 --oviposition $oviposition 41 --oviposition $oviposition
22 --photoperiod $photoperiod 42 --photoperiod $photoperiod
23 --replications $replications 43 --replications $replications
24 --std_error_plot $std_error_plot 44 --plot_generations_separately $plot_generations_separately
45 --plot_std_error $plot_std_error
25 --young_nymph_accumulation $young_nymph_accumulation]]></command> 46 --young_nymph_accumulation $young_nymph_accumulation]]></command>
26 <inputs> 47 <inputs>
27 <param name="input" type="data" format="csv" label="Temperature data" /> 48 <param name="input" type="data" format="csv" label="Temperature data" />
28 <param name="location" type="text" value="" optional="false" label="Location" /> 49 <param name="location" type="text" value="" optional="false" label="Location" />
29 <param name="insect" type="select" label="Select insect"> 50 <param name="insect" type="select" label="Select insect">
30 <option value="Brown Marmorated Stink Bug" selected="True">Brown Marmorated Stink Bug</option> 51 <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
31 </param> 52 </param>
32 <param name="replications" type="integer" value="10" min="1" label="Number of replications" /> 53 <param name="replications" type="integer" value="10" min="2" label="Number of replications" />
33 <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication" /> 54 <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication" />
34 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> 55 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
35 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> 56 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
36 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> 57 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
37 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> 58 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
39 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" /> 60 <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
40 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" /> 61 <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
41 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" /> 62 <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" />
42 <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" /> 63 <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" />
43 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" /> 64 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" />
44 <param name="std_error_plot" type="select" label="Plot standard error?"> 65 <param name="plot_generations_separately" type="select" label="Plot generations separately?">
45 <option value="1" selected="True">Yes</option> 66 <option value="yes" selected="True">Yes</option>
46 <option value="0">No</option> 67 <option value="no">No</option>
68 </param>
69 <conditional name="life_stages_cond" label="Select life_stages for plotting">
70 <param name="life_stages" type="select" label="Select life stages for plotting">
71 <option value="Total" selected="true">All</option>
72 <option value="Egg">Egg</option>
73 <option value="Nymph">Nymph</option>
74 <option value="Adult">Adult</option>
75 </param>
76 <when value="Total"/>
77 <when value="Egg"/>
78 <when value="Nymph">
79 <param name="life_stage_nymph" type="select" label="Select nymph life stage">
80 <option value="Total" selected="true">All</option>
81 <option value="Young">Young</option>
82 <option value="Old">Old</option>
83 </param>
84 </when>
85 <when value="Adult">
86 <param name="life_stages_adult" type="select" label="Select adult life stage">
87 <option value="Total" selected="true">All</option>
88 <option value="Pre-vittelogenic">Pre-vittelogenic</option>
89 <option value="Vittelogenic">Vittelogenic</option>
90 <option value="Diapausing">Diapausing</option>
91 </param>
92 </when>
93 </conditional>
94 <param name="plot_std_error" type="select" label="Plot standard error?">
95 <option value="yes" selected="True">Yes</option>
96 <option value="no">No</option>
47 </param> 97 </param>
48 </inputs> 98 </inputs>
49 <outputs> 99 <outputs>
50 <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" /> 100 <collection name="output_collection" type="list" label="${tool.name} ${location}, on ${on_string}">
101 <discover_datasets pattern="__name__" directory="output_dir" format="pdf" />
102 </collection>
51 </outputs> 103 </outputs>
52 <tests> 104 <tests>
53 <test> 105 <test>
54 <param name="input" value="state_college.csv" ftype="csv" /> 106 <param name="input" value="state_college.csv" ftype="csv" />
55 <param name="location" value="State College PA" /> 107 <param name="location" value="State College PA" />
56 <param name="replications" value="10" /> 108 <param name="replications" value="10" />
57 <output name="output" file="output.pdf" ftype="pdf" compare="contains" /> 109 <output_collection name="output_collection" type="list">
110 <element name="output.pdf" file="output.pdf" ftype="pdf" compare="contains"/>
111 </output_collection>
58 </test> 112 </test>
59 </tests> 113 </tests>
60 <help> 114 <help>
61 **What it does** 115 **What it does**
62 116
79 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size. 133 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
80 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size 134 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
81 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph). 135 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
82 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph). 136 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
83 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult). 137 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
138 * **Plot generations separately** - select "Yes" to plot P, F1 and F2 as separate lines or "no" to pool across generations, resulting in a total for the selected life states.
139 * **Select life stages for plotting** - select any combinaton of Egg, Nymph, Adult or "All" for plotting.
84 * **Plot standard error** - add standard error lines to plot. 140 * **Plot standard error** - add standard error lines to plot.
85 141
86 </help> 142 </help>
87 <citations> 143 <citations>
88 <citation type="doi">10.3389/fphys.2016.00165</citation> 144 <citation type="doi">10.3389/fphys.2016.00165</citation>