annotate glmmpql.xml @ 0:f3e1b6d244a6 draft default tip

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

<tool id="regionalgam_glmmpql" name="Expected temporal trend" version="@VERSION@">
    <description>of species abundance</description>
    <macros>
        <import>regionalgam_macros.xml</import>
    </macros>
    <expand macro="rg_nlme_mass_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/glmmpql.R' 
            '$ab_indices' 
            '$output' '$output2' 
    ]]>
    </command>
    <inputs>
        <expand macro="rg_ab_indices"/>
    </inputs>
    <outputs>
        <data format="png" name="output" from_work_dir="output-plot.png" />
        <data format="tabular" name="output2" from_work_dir="output-glmmpql" />
    </outputs>
    <tests>
        <test>
            <param name="ab_indices" value="s_data_index.tabular"/>
            <output name="output2" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="5.5.*"/>
                    <has_line line="&quot;x&quot;"/>
                    <has_n_columns n="1"/>
                </assert_contents>
            </output>   
        </test>
    </tests>
    <help><![CDATA[
=====================================
Temporal trends of species abundance
=====================================

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

This function computes a collated index for each year and estimates the temporal trend.

A collated index correspond to the expected value for a year, when taking into account the variation contained among sites. 

Here we also add an autoregressive term to account for temporal autocorrelation in the time series.

|

**Outputs**

The tool returns the collated index in tabular format.

It also and plot it against year for visualization in an output png file.

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