comparison insect_phenology_model.xml @ 3:24fa0d35a8bf draft

Uploaded

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" />
            <param name="year" value="2014" />
            <param name="replications" value="3" />
            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
        </test>
    </tests>
    <help>
**What it does**

**Required options**

 * **Location** - the location associated with the selected temperature data.
 * **Temperature data** - select the dataset from your history containing the temperature data.
 * **Temperature data year** - the year during which the temperature data was recorded.
 * **Number of replications** - number of replications.
 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.

 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
 
    </help>
    <citations>
        <citation type="doi">10.3389/fphys.2016.00165</citation>
    </citations>
</tool>

3:24fa0d35a8bf

<?xml version="."?>
<tool id="insect_phenology_model" name="Insect phenology model" version="1.1.0">
    <description>expressing stage-specific phenology and population dynamics</description>
    <requirements>
         <requirement type="package" version="1.4.4">r-optparse</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/insect_phenology_model.R'
-a $adult_mort
-b $adult_accum
-c $egg_mort
-e '$location'
-f $max_clutch_size
-i $min_clutch_size
-j $nymph_mort
-k $old_nymph_accum
-n $input.metadata.data_lines
-o '$output'
-p $oviposition
-q $photoperiod
-s $replications
-t $se_plot
-v '$input'
-y $young_nymph_accum
    ]]></command>
    <inputs>
        <param name="location" type="text" value="" optional="false" label="Location" />
        <param name="input" type="data" format="csv" label="Temperature data" />
        <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}, on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="state_college.csv" ftype="csv" />
            <param name="location" value="State College PA" />
            <param name="replications" value="10" />
            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
        </test>
    </tests>
    <help>
**What it does**

**Required options**

 * **Location** - the location associated with the selected temperature data.
 * **Temperature data** - select the dataset from your history containing the temperature data.
 * **Number of replications** - number of replications.
 * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
 * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
 * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
 * **Adjustment rate for adult mortality** - adjustment rate for adult mortality.

 * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
 
    </help>
    <citations>
        <citation type="doi">10.3389/fphys.2016.00165</citation>
        <citation type="doi">10.1175/JTECH-D-11-00103.1</citation>
        <citation type="doi">10.7289/V5D21VHZ</citation>
    </citations>
</tool>