view flight_curve_en.xml @ 0:5b126f770671 draft

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<tool id="flight-curve" name="Flight curve">
<description>compute the regional expected pattern of abundance</description>
    <requirements>
        <requirement type="package" version="3.4">r</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/flight_curve.R' '$__tool_directory__/dennis_gam_initial_functions.R' '$input' '$output' ]]>
    </command>
    <inputs>
        <param format="tabular,csv" name="input" type="data" label="Count file" help="The file must contain the SPECIES, SITE, YEAR, MONTH, DAY and COUNT columns. CSV file separator ',' or tab."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" from_work_dir="pheno" />
    </outputs>
    <tests>
        <test> <!--FAILED-->
            <param name="input" value="gatekeeper_CM"/>
            <output name="output" value="flight_curve_result.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
    
.. class:: infomark 

==========================
Regional phenology
==========================

This tool is an implementation of the flight_curve function `RegionalGAM package:  https://github.com/RetoSchmucki/regionalGAM/
This function computes the annual phenology on a specific region.

    ]]></help>
    <citations>
        <citation type="doi">10.1111/1365-2664.12561</citation>  
    </citations>
</tool>