Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.xml @ 17:6f31ade9a0f4 draft

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author greg
date Tue, 06 Mar 2018 08:26:50 -0500
parents 4aadc28100b0
children f5ecff4800f2
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16:309954bbe999 17:6f31ade9a0f4
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_stage_nymph = "None" 7 #set life_stages = list()
8 #set life_stages_adult = "None"
9 #set stages = list()
10 #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage 8 #set plot_adult_life_stage = $plot_adult_life_stage_cond.plot_adult_life_stage
11 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage 9 #set plot_nymph_life_stage = $plot_nymph_life_stage_cond.plot_nymph_life_stage
10 #if str($plot_egg_life_stage) == "yes":
11 $life_stages.append("Egg")
12 #end if
13 #if str($plot_nymph_life_stage) == "yes":
14 $life_stages.append("Nymph")
15 #end if
16 #if str($plot_adult_life_stage) == "yes":
17 $life_stages.append("Adult")
18 #end if
12 #if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes": 19 #if str($plot_egg_life_stage) == "yes" and str($plot_nymph_life_stage) == "yes" and str($plot_adult_life_stage) == "yes":
13 $stages.append("Total") 20 $life_stages.append("Total")
14 #set life_stage_nymph = $plot_nymph_life_stage_cond.life_stage_nymph
15 #set life_stages_adult = $plot_adult_life_stage_cond.life_stages_adult
16 #else:
17 #if str($plot_egg_life_stage) == "yes":
18 $stages.append("Egg")
19 #end if
20 #if str($plot_nymph_life_stage) == "yes":
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 = $plot_adult_life_stage_cond.life_stages_adult
27 #end if
28 #end if 21 #end if
29 #set stages = ",".join($stages) 22 #set life_stages = ",".join($life_stages)
30 mkdir output_dir && 23 mkdir output_dir &&
31 Rscript '$__tool_directory__/insect_phenology_model.R' 24 Rscript '$__tool_directory__/insect_phenology_model.R'
32 --adult_mortality $adult_mortality 25 --adult_mortality $adult_mortality
33 --adult_accumulation $adult_accumulation 26 --adult_accumulation $adult_accumulation
34 --egg_mortality $egg_mortality 27 --egg_mortality $egg_mortality
35 --input '$input' 28 --input '$input'
36 --insect '$insect' 29 --insect '$insect'
37 --insects_per_replication $insects_per_replication 30 --insects_per_replication $insects_per_replication
38 --life_stages '$stages' 31 --life_stages '$life_stages'
39 #if str($life_stages_adult) != "None": 32 #if str($plot_adult_life_stage) == "yes":
40 --life_stages_adult $life_stages_adult 33 --life_stages_adult '$plot_adult_life_stage_cond.life_stages_adult'
41 #end if 34 #end if
42 #if str($life_stage_nymph) != "None": 35 #if str($plot_nymph_life_stage) == "yes":
43 --life_stage_nymph $life_stage_nymph 36 --life_stages_nymph '$plot_nymph_life_stage_cond.life_stages_nymph'
44 #end if 37 #end if
45 --location '$location' 38 --location '$location'
46 --max_clutch_size $max_clutch_size 39 --max_clutch_size $max_clutch_size
47 --min_clutch_size $min_clutch_size 40 --min_clutch_size $min_clutch_size
48 --nymph_mortality $nymph_mortality 41 --nymph_mortality $nymph_mortality
84 <param name="plot_nymph_life_stage" type="select" label="Plot nymph life stage?"> 77 <param name="plot_nymph_life_stage" type="select" label="Plot nymph life stage?">
85 <option value="yes" selected="true">Yes</option> 78 <option value="yes" selected="true">Yes</option>
86 <option value="no">No</option> 79 <option value="no">No</option>
87 </param> 80 </param>
88 <when value="yes"> 81 <when value="yes">
89 <param name="life_stage_nymph" type="select" label="Select nymph life stage"> 82 <param name="life_stages_nymph" type="select" multiple="true" label="Select nymph life stage">
90 <option value="Total" selected="true">All</option> 83 <option value="Total" selected="true">All</option>
91 <option value="Young">Young</option> 84 <option value="Young">Young</option>
92 <option value="Old">Old</option> 85 <option value="Old">Old</option>
93 </param> 86 </param>
94 </when> 87 </when>
98 <param name="plot_adult_life_stage" type="select" label="Plot adult life stage?"> 91 <param name="plot_adult_life_stage" type="select" label="Plot adult life stage?">
99 <option value="yes" selected="true">Yes</option> 92 <option value="yes" selected="true">Yes</option>
100 <option value="no">No</option> 93 <option value="no">No</option>
101 </param> 94 </param>
102 <when value="yes"> 95 <when value="yes">
103 <param name="life_stages_adult" type="select" label="Select adult life stage"> 96 <param name="life_stages_adult" type="select" multiple="true" label="Select adult life stage">
104 <option value="Total" selected="true">All</option> 97 <option value="Total" selected="true">All</option>
105 <option value="Pre-vittelogenic">Pre-vittelogenic</option> 98 <option value="Pre-vittelogenic">Pre-vittelogenic</option>
106 <option value="Vittelogenic">Vittelogenic</option> 99 <option value="Vittelogenic">Vittelogenic</option>
107 <option value="Diapausing">Diapausing</option> 100 <option value="Diapausing">Diapausing</option>
108 </param> 101 </param>