Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.xml @ 108:9d5824e4b5d0 draft

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author greg
date Tue, 05 Dec 2017 15:15:49 -0500
parents 375a2b8e7207
children 1e28f7f61bb0
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107:2c2903e7ce68 108:9d5824e4b5d0
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 Rscript '$__tool_directory__/insect_phenology_model.R' 7 Rscript '$__tool_directory__/insect_phenology_model.R'
8 -a $adult_mortality 8 --adult_mortality $adult_mortality
9 -b $adult_accumulation 9 --adult_accumulation $adult_accumulation
10 -c $egg_mortality 10 --egg_mortality $egg_mortality
11 -e '$location' 11 --input '$input'
12 -f $max_clutch_size 12 --insect '$insect'
13 -i $min_clutch_size 13 --insects_per_replication $insects_per_replication
14 -j $nymph_mortality 14 --location '$location'
15 -k $old_nymph_accumulation 15 --max_clutch_size $max_clutch_size
16 -n $input.metadata.data_lines 16 --min_clutch_size $min_clutch_size
17 -o '$output' 17 --nymph_mortality $nymph_mortality
18 -p $oviposition 18 --num_days $input.metadata.data_lines
19 -q $photoperiod 19 --old_nymph_accumulation $old_nymph_accumulation
20 -s $replications 20 --output '$output'
21 -t $std_error_plot 21 --oviposition $oviposition
22 -v '$input' 22 --photoperiod $photoperiod
23 -y $young_nymph_accumulation 23 --replications $replications
24 -x '$insect']]></command> 24 --std_error_plot $std_error_plot
25 --young_nymph_accumulation $young_nymph_accumulation]]></command>
25 <inputs> 26 <inputs>
26 <param name="input" type="data" format="csv" label="Temperature data" /> 27 <param name="input" type="data" format="csv" label="Temperature data" />
27 <param name="location" type="text" value="" optional="false" label="Location" /> 28 <param name="location" type="text" value="" optional="false" label="Location" />
28 <param name="insect" type="select" label="Select insect"> 29 <param name="insect" type="select" label="Select insect">
29 <option value="Brown Marmolated Stink Bug" selected="True">Brown Marmolated Stink Bug</option> 30 <option value="Brown Marmolated Stink Bug" selected="True">Brown Marmolated Stink Bug</option>
30 </param> 31 </param>
31 <param name="replications" type="integer" value="10" min="1" label="Number of replications" /> 32 <param name="replications" type="integer" value="10" min="1" 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" />
32 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> 34 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
33 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> 35 <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
34 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> 36 <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
35 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> 37 <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
36 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" /> 38 <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
64 66
65 **Required options** 67 **Required options**
66 68
67 * **Location** - the location associated with the selected temperature data. 69 * **Location** - the location associated with the selected temperature data.
68 * **Temperature data** - select the dataset from your history containing the temperature data. 70 * **Temperature data** - select the dataset from your history containing the temperature data.
71 * **Select insect** - currently only the Brown Marmolated Stink Bug can be analyzed.
69 * **Number of replications** - number of replications. 72 * **Number of replications** - number of replications.
73 * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects.
70 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination. 74 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
71 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality. 75 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
72 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality. 76 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
73 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality. 77 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
74 * **Adjustment oviposition rate** - adjustment oviposition rate. 78 * **Adjustment oviposition rate** - adjustment oviposition rate.
75 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size. 79 * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
76 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size 80 * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
77 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph). 81 * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
78 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph). 82 * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
79 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult). 83 * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
80 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults. 84 * **Plot standard error** - add standard error lines to plot.
81 85
82 </help> 86 </help>
83 <citations> 87 <citations>
84 <citation type="doi">10.3389/fphys.2016.00165</citation> 88 <citation type="doi">10.3389/fphys.2016.00165</citation>
85 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation> 89 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>