<tool id="glmmpql" name="Expected temporal trend" version="0.1">
    <description>of species abundance</description>
    <requirements>
        <requirement type="package" version="3.1_131">r-nlme</requirement>
        <requirement type="package" version="7.3_48">r-mass</requirement>
        <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
        <requirement type="package" version="1.2.2">xorg-libsm</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/glmmpql.R' '$input1' '$output' '$output2' ]]>
    </command>
    <inputs>
        <param format="tabular" name="input1" type="data" label="Tabular file generated by the ab_index tool"/>
    </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="input1" value="data_index.tabular"/>
            <param name="output" value="glmmpql-plot.png"/>
            <output name="output2" value="glmmpql.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
    
.. class:: infomark 

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