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comparison insect_phenology_model.xml @ 3:24fa0d35a8bf draft

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author greg
date Thu, 09 Nov 2017 14:20:42 -0500
parents 07444af6824f
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2:07444af6824f 3:24fa0d35a8bf
1 <?xml version="."?> 1 <?xml version="."?>
2 <tool id="insect_phenology_model" name="Insect phenology model" version="1.0.0"> 2 <tool id="insect_phenology_model" name="Insect phenology model" version="1.1.0">
3 <description>expressing stage-specific phenology and population dynamics</description> 3 <description>expressing stage-specific phenology and population dynamics</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.3.2">r-optparse</requirement> 5 <requirement type="package" version="1.4.4">r-optparse</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$__tool_directory__/insect_phenology_model.R' 8 Rscript '$__tool_directory__/insect_phenology_model.R'
9 -a $adult_mort 9 -a $adult_mort
10 -b $adult_accum 10 -b $adult_accum
11 -c $egg_mort 11 -c $egg_mort
12 -d $latitude
13 -e '$location' 12 -e '$location'
14 -f $max_clutch_size 13 -f $max_clutch_size
15 -i $min_clutch_size 14 -i $min_clutch_size
16 -j $nymph_mort 15 -j $nymph_mort
17 -k $old_nymph_accum 16 -k $old_nymph_accum
17 -n $input.metadata.data_lines
18 -o '$output' 18 -o '$output'
19 -p $oviposition 19 -p $oviposition
20 -q $photoperiod 20 -q $photoperiod
21 -s $replications 21 -s $replications
22 -t $se_plot 22 -t $se_plot
23 -u $year 23 -v '$input'
24 -v '$temperature_data'
25 -y $young_nymph_accum 24 -y $young_nymph_accum
26 ]]></command> 25 ]]></command>
27 <inputs> 26 <inputs>
28 <param name="location" type="text" value="" optional="false" label="Location" /> 27 <param name="location" type="text" value="" optional="false" label="Location" />
29 <param name="latitude" type="float" value="0.0" label="Latitude of selected location" /> 28 <param name="input" type="data" format="csv" label="Temperature data" />
30 <param name="temperature_data" type="data" format="csv" label="Temperature data" />
31 <param name="year" type="integer" value="2017" min="1995" label="Temperature data year" />
32 <param name="replications" type="integer" value="10" min="1" label="Number of replications" /> 29 <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
33 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> 30 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
34 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> 31 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
35 <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> 32 <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
36 <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> 33 <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
44 <option value="1" selected="True">Yes</option> 41 <option value="1" selected="True">Yes</option>
45 <option value="0">No</option> 42 <option value="0">No</option>
46 </param> 43 </param>
47 </inputs> 44 </inputs>
48 <outputs> 45 <outputs>
49 <data name="output" format="pdf" label="${tool.name} ${location}, ${year} lat:${latitude} on ${on_string}" /> 46 <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" />
50 </outputs> 47 </outputs>
51 <tests> 48 <tests>
52 <test> 49 <test>
53 <param name="temperature_data" value="asheville2014.csv" ftype="csv" /> 50 <param name="input" value="state_college.csv" ftype="csv" />
54 <param name="location" value="asheville:35.58" /> 51 <param name="location" value="State College PA" />
55 <param name="year" value="2014" /> 52 <param name="replications" value="10" />
56 <param name="replications" value="3" />
57 <output name="output" file="output.pdf" ftype="pdf" compare="contains" /> 53 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
58 </test> 54 </test>
59 </tests> 55 </tests>
60 <help> 56 <help>
61 **What it does** 57 **What it does**
66 62
67 **Required options** 63 **Required options**
68 64
69 * **Location** - the location associated with the selected temperature data. 65 * **Location** - the location associated with the selected temperature data.
70 * **Temperature data** - select the dataset from your history containing the temperature data. 66 * **Temperature data** - select the dataset from your history containing the temperature data.
71 * **Temperature data year** - the year during which the temperature data was recorded.
72 * **Number of replications** - number of replications. 67 * **Number of replications** - number of replications.
73 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination. 68 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
74 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality. 69 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
75 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality. 70 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
76 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality. 71 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.
83 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults. 78 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
84 79
85 </help> 80 </help>
86 <citations> 81 <citations>
87 <citation type="doi">10.3389/fphys.2016.00165</citation> 82 <citation type="doi">10.3389/fphys.2016.00165</citation>
83 <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
84 <citation type="doi">10.7289/V5D21VHZ</citation>
88 </citations> 85 </citations>
89 </tool> 86 </tool>