comparison insect_phenology_model.xml @ 2:07444af6824f draft

Uploaded

1:3debfb664792

<?xml version="."?>
<tool id="insect_phenology_model" name="Insect phenology model" version="1.0.0">
    <description>expressing stage-specific phenology and population dynamics</description>
    <requirements>
         <requirement type="package" version="1.3.0">r-optparse</requirement>
    </requirements>
    <command><![CDATA[
#set loc_lat_items = str($location).split(':')
#set loc = $loc_lat_items[0]
#set lat = $loc_lat_items[1]
Rscript '$__tool_directory__/insect_phenology_model.R'
-a $adult_mort
-b $adult_accum
-c $egg_mort
-d $lat
-e $loc
-f $max_clutch_size
-i $min_clutch_size
-j $nymph_mort
-k $old_nymph_accum
-o $output
-p $oviposition
-q $photoperiod
-s $replications
-t $se_plot
-u $year
-v '$temperature_data'
-y $young_nymph_accum
    ]]></command>
    <inputs>
        <param name="location" type="select" label="Location">
            <options from_file="locations.txt">
                <column name="name" index="0"/>
                <column name="value" index="1"/>
            </options>
        </param>
        <param name="temperature_data" type="data" format="csv" label="Temperature data" />
        <param name="year" type="select" label="Temperature data year">
            <options from_file="years.txt">
                <column name="name" index="0"/>
                <column name="value" index="1"/>
            </options>
        </param>
        <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
        <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
        <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
        <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
        <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />

            <option value="1" selected="True">Yes</option>
            <option value="0">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="pdf" label="${tool.name} ${str($location).split(':')[0]}, ${year} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="temperature_data" value="asheville2014.csv" ftype="csv" />
            <param name="location" value="asheville:35.58" />

2:07444af6824f

<?xml version="."?>
<tool id="insect_phenology_model" name="Insect phenology model" version="1.0.0">
    <description>expressing stage-specific phenology and population dynamics</description>
    <requirements>
         <requirement type="package" version="1.3.2">r-optparse</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/insect_phenology_model.R'
-a $adult_mort
-b $adult_accum
-c $egg_mort
-d $latitude
-e '$location'
-f $max_clutch_size
-i $min_clutch_size
-j $nymph_mort
-k $old_nymph_accum
-o '$output'
-p $oviposition
-q $photoperiod
-s $replications
-t $se_plot
-u $year
-v '$temperature_data'
-y $young_nymph_accum
    ]]></command>
    <inputs>
        <param name="location" type="text" value="" optional="false" label="Location" />
        <param name="latitude" type="float" value="0.0" label="Latitude of selected location" />
        <param name="temperature_data" type="data" format="csv" label="Temperature data" />
        <param name="year" type="integer" value="2017" min="1995" label="Temperature data year" />
        <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
        <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
        <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
        <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
        <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />

            <option value="1" selected="True">Yes</option>
            <option value="0">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="pdf" label="${tool.name} ${location}, ${year} lat:${latitude} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="temperature_data" value="asheville2014.csv" ftype="csv" />
            <param name="location" value="asheville:35.58" />