Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.xml @ 13:8f7d918586bc draft

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author greg
date Wed, 28 Feb 2018 13:39:44 -0500
parents bd5e35775e20
children 4aadc28100b0
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12:bd5e35775e20 13:8f7d918586bc
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 life_stages_nymph = "None"
8 #set life_stages_adult = "None"
7 #set stages = list() 9 #set stages = list()
8 #set life_stages_adult = "None" 10 #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage
9 #set life_stage_nymph = "None" 11 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage
10 #set life_stages = $life_stages_cond.life_stages 12 #if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes":
11 #for life_stage in str($life_stages).split(","): 13 $stages.append("Total")
12 #if $life_stage == "Adult": 14 #set life_stage_nymph = $plot_nymph_life_stage_cond.life_stage_nymph
13 #set life_stages_adult = $life_stages_cond.life_stages_adult 15 #set life_stages_adult = $plot_adult_life_stage_cond.life_stages_adult
14 #else if $life_stage == "Nymph": 16 #else:
15 #set life_stage_nymph = $life_stages_cond.life_stage_nymph 17 #if str($plot_egg_life_stage) == "yes":
18 $stages.append("Egg")
16 #end if 19 #end if
17 $stages.append($life_stage) 20 #if str($plot_nymph_life_stage) == "yes":
18 #end for 21 $stages.append("Nymph")
22 #set life_stage_nymph = $plot_nymph_life_stage_cond.life_stage_nymph
23 #end if
24 #if str($plot_adult_life_stage) == "yes":
25 $stages.append("Adult")
26 #set life_stages_adult = $plot_adult_life_stage_cond.life_stages_adult
27 #end if
28 #end if
19 #set stages = ",".join($stages) 29 #set stages = ",".join($stages)
20 mkdir output_dir && 30 mkdir output_dir &&
21 Rscript '$__tool_directory__/insect_phenology_model.R' 31 Rscript '$__tool_directory__/insect_phenology_model.R'
22 --adult_mortality $adult_mortality 32 --adult_mortality $adult_mortality
23 --adult_accumulation $adult_accumulation 33 --adult_accumulation $adult_accumulation
27 --insects_per_replication $insects_per_replication 37 --insects_per_replication $insects_per_replication
28 --life_stages '$stages' 38 --life_stages '$stages'
29 #if str($life_stages_adult) != "None": 39 #if str($life_stages_adult) != "None":
30 --life_stages_adult $life_stages_adult 40 --life_stages_adult $life_stages_adult
31 #end if 41 #end if
32 #if str($life_stage_nymph) != "None": 42 #if str($life_stage_nymph) != "no":
33 --life_stage_nymph $life_stage_nymph 43 --life_stage_nymph $life_stage_nymph
34 #end if 44 #end if
35 --location '$location' 45 --location '$location'
36 --max_clutch_size $max_clutch_size 46 --max_clutch_size $max_clutch_size
37 --min_clutch_size $min_clutch_size 47 --min_clutch_size $min_clutch_size
64 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" /> 74 <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" />
65 <param name="plot_generations_separately" type="select" label="Plot generations separately?"> 75 <param name="plot_generations_separately" type="select" label="Plot generations separately?">
66 <option value="yes" selected="True">Yes</option> 76 <option value="yes" selected="True">Yes</option>
67 <option value="no">No</option> 77 <option value="no">No</option>
68 </param> 78 </param>
69 <conditional name="life_stages_cond" label="Select life_stages for plotting"> 79 <param name="plot_egg_life_stage" type="select" label="Plot egg life stage?">
70 <param name="life_stages" type="select" label="Select life stages for plotting"> 80 <option value="yes" selected="true">Yes</option>
71 <option value="Total" selected="true">All</option> 81 <option value="no">No</option>
72 <option value="Egg">Egg</option> 82 </param>
73 <option value="Nymph">Nymph</option> 83 <conditional name="plot_nymph_life_stage_cond">
74 <option value="Adult">Adult</option> 84 <param name="plot_nymph_life_stage" type="select" label="Plot nymph life stage?">
85 <option value="yes" selected="true">Yes</option>
86 <option value="no">No</option>
75 </param> 87 </param>
76 <when value="Total"/> 88 <when value="yes">
77 <when value="Egg"/>
78 <when value="Nymph">
79 <param name="life_stage_nymph" type="select" label="Select nymph life stage"> 89 <param name="life_stage_nymph" type="select" label="Select nymph life stage">
80 <option value="Total" selected="true">All</option> 90 <option value="Total" selected="true">All</option>
81 <option value="Young">Young</option> 91 <option value="Young">Young</option>
82 <option value="Old">Old</option> 92 <option value="Old">Old</option>
83 </param> 93 </param>
84 </when> 94 </when>
85 <when value="Adult"> 95 <when value="no"/>
96 </conditional>
97 <conditional name="plot_adult_life_stage_cond">
98 <param name="plot_adult_life_stage" type="select" label="Plot adult life stage?">
99 <option value="yes" selected="true">Yes</option>
100 <option value="no">No</option>
101 </param>
102 <when value="yes">
86 <param name="life_stages_adult" type="select" label="Select adult life stage"> 103 <param name="life_stages_adult" type="select" label="Select adult life stage">
87 <option value="Total" selected="true">All</option> 104 <option value="Total" selected="true">All</option>
88 <option value="Pre-vittelogenic">Pre-vittelogenic</option> 105 <option value="Pre-vittelogenic">Pre-vittelogenic</option>
89 <option value="Vittelogenic">Vittelogenic</option> 106 <option value="Vittelogenic">Vittelogenic</option>
90 <option value="Diapausing">Diapausing</option> 107 <option value="Diapausing">Diapausing</option>
91 </param> 108 </param>
92 </when> 109 </when>
110 <when value="no"/>
93 </conditional> 111 </conditional>
94 <param name="plot_std_error" type="select" label="Plot standard error?"> 112 <param name="plot_std_error" type="select" label="Plot standard error?">
95 <option value="yes" selected="True">Yes</option> 113 <option value="yes" selected="True">Yes</option>
96 <option value="no">No</option> 114 <option value="no">No</option>
97 </param> 115 </param>