annotate flight-curve.xml @ 0:fff507f00b2b draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e

<tool id="regionalgam_flight_curve" name="Flight curve" version="@VERSION@">
    <description>compute the regional expected pattern of abundance</description>
    <macros>
        <import>regionalgam_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.8_28">r-mgcv</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/flight-curve.R' 
            '$__tool_directory__/dennis-gam-initial-functions.R' 
            '$count_file' 
            $minvisit 
            $minoccur 
            '$output' 
    ]]>
    </command>
    <inputs>
        <expand macro="rg_count_file"/>
        <param name="minvisit" type="integer" value="3" min="0" label="Minimum number of visits" help="Subset the data with a minimum number of visits." />
        <param name="minoccur" type="integer" value="2" min="0" label="Minimum number of occurences" help="Subset the data with a minimum number of occurences."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" from_work_dir="pheno" />
    </outputs>
    <tests>
        <test>
            <param name="count_file" value="gatekeeper_CM_200320042005"/>
            <param name="minvisit" value="3"/>
            <param name="minoccur" value="2"/>
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_line line="&quot;species&quot;&#009;&quot;year&quot;&#009;&quot;week&quot;&#009;&quot;DAYNO&quot;&#009;&quot;DAYNO_adj&quot;&#009;&quot;nm&quot;"/>
                    <has_n_columns n="6"/>
                    <has_text_matching expression="&quot;Pyronia&#032;tithonus&quot;&#009;2003&#009;[0-9]&#009;[0-9]&#009;[0-9]&#009;[0-9]"/>
                </assert_contents>
            </output>   
        </test>
    </tests>
    <help><![CDATA[
==========================
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.

The output tabular file can be used to impute expected count values with the abundance index computation tool. 

|

**Outputs**

Regional expected pattern computation in a tabular file.
    ]]></help>
    <expand macro="rg_citation"/>
</tool>