annotate ab-index.xml @ 0:d0ee713d4758 draft default tip

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

<tool id="regionalgam_ab_index" name="Abundance index" version="@VERSION@">
    <description>computation across species, sites and years</description>
    <macros>
        <import>regionalgam_macros.xml</import>
    </macros>
    <expand macro="rg_r_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/ab-index.R'
            '$__tool_directory__/dennis-gam-initial-functions.R' 
            '$count_file' '$input2' 
            '$output' 
    ]]>
    </command>
    <inputs>
        <expand macro="rg_count_file"/>
        <param format="tabular" name="input2" type="data" label="Regional expected pattern of abundance" help="Flight curve output, tabular file."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" from_work_dir="data.index" />
    </outputs>
    <tests>
        <test>
            <param name="count_file" value="gatekeeper_CM_200320042005"/>
            <param name="input2" value="s_flight_curve_result.tabular"/>
            <output name="output" file="s_data_index.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
==========================
Compute abundance index
==========================

This tool is an implementation of the abundance_index function from RegionalGAM package:  https://github.com/RetoSchmucki/regionalGAM/

This function compute the Abundance Index across sites and years from your dataset and the regional flight curve.

|

**Outputs**

The tool returns computed abundance indices in tabular format.

    ]]></help>
    <expand macro="rg_citation"/>
</tool>