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comparison insect_phenology_model.xml @ 2:07444af6824f draft

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author greg
date Mon, 14 Aug 2017 13:47:50 -0400
parents 244c373f2a34
children 24fa0d35a8bf
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1:3debfb664792 2:07444af6824f
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="1.0.0">
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="1.3.0">r-optparse</requirement> 5 <requirement type="package" version="1.3.2">r-optparse</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #set loc_lat_items = str($location).split(':')
9 #set loc = $loc_lat_items[0]
10 #set lat = $loc_lat_items[1]
11 Rscript '$__tool_directory__/insect_phenology_model.R' 8 Rscript '$__tool_directory__/insect_phenology_model.R'
12 -a $adult_mort 9 -a $adult_mort
13 -b $adult_accum 10 -b $adult_accum
14 -c $egg_mort 11 -c $egg_mort
15 -d $lat 12 -d $latitude
16 -e $loc 13 -e '$location'
17 -f $max_clutch_size 14 -f $max_clutch_size
18 -i $min_clutch_size 15 -i $min_clutch_size
19 -j $nymph_mort 16 -j $nymph_mort
20 -k $old_nymph_accum 17 -k $old_nymph_accum
21 -o $output 18 -o '$output'
22 -p $oviposition 19 -p $oviposition
23 -q $photoperiod 20 -q $photoperiod
24 -s $replications 21 -s $replications
25 -t $se_plot 22 -t $se_plot
26 -u $year 23 -u $year
27 -v '$temperature_data' 24 -v '$temperature_data'
28 -y $young_nymph_accum 25 -y $young_nymph_accum
29 ]]></command> 26 ]]></command>
30 <inputs> 27 <inputs>
31 <param name="location" type="select" label="Location"> 28 <param name="location" type="text" value="" optional="false" label="Location" />
32 <options from_file="locations.txt"> 29 <param name="latitude" type="float" value="0.0" label="Latitude of selected location" />
33 <column name="name" index="0"/>
34 <column name="value" index="1"/>
35 </options>
36 </param>
37 <param name="temperature_data" type="data" format="csv" label="Temperature data" /> 30 <param name="temperature_data" type="data" format="csv" label="Temperature data" />
38 <param name="year" type="select" label="Temperature data year"> 31 <param name="year" type="integer" value="2017" min="1995" label="Temperature data year" />
39 <options from_file="years.txt">
40 <column name="name" index="0"/>
41 <column name="value" index="1"/>
42 </options>
43 </param>
44 <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" />
45 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" /> 33 <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
46 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" /> 34 <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
47 <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" /> 35 <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
48 <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" /> 36 <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
56 <option value="1" selected="True">Yes</option> 44 <option value="1" selected="True">Yes</option>
57 <option value="0">No</option> 45 <option value="0">No</option>
58 </param> 46 </param>
59 </inputs> 47 </inputs>
60 <outputs> 48 <outputs>
61 <data name="output" format="pdf" label="${tool.name} ${str($location).split(':')[0]}, ${year} on ${on_string}" /> 49 <data name="output" format="pdf" label="${tool.name} ${location}, ${year} lat:${latitude} on ${on_string}" />
62 </outputs> 50 </outputs>
63 <tests> 51 <tests>
64 <test> 52 <test>
65 <param name="temperature_data" value="asheville2014.csv" ftype="csv" /> 53 <param name="temperature_data" value="asheville2014.csv" ftype="csv" />
66 <param name="location" value="asheville:35.58" /> 54 <param name="location" value="asheville:35.58" />