<tool id="gls-adjusted" name="Linear regression ajusted" version="0.1">
    <description>for autocorrelation in the residuals</description>
    <requirements>
        <requirement type="package" version="3.1_131">r-nlme</requirement>
        <requirement type="package" version="7.3_48">r-mass</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/gls-adjusted.R' '$input1' '$input2' '$output' '$output2' ]]>
    </command>
    <inputs>
        <param format="tabular" name="input1" type="data" label="File generated by the glmmpql/Expected temporal trend tool"/>
        <param format="tabular" name="input2" type="data" label="File generated by the ab_index tool"/>
    </inputs>
    <outputs>
        <data format="txt" name="output" from_work_dir="mod_adjusted-summary.txt" />
        <data format="rdata" name="output2" from_work_dir="mod_adjusted.rda" />
    </outputs>
    <tests>
        <test> <!--FAILED-->
            <param name="input1" value="glmmpql.tabular"/>
            <param name="input2" value="data_index.tabular"/>
            <output name="output" value="gls-adju_sum.txt"/>
            <output name="output2" value="gls-adju_rda.rda"/>
        </test>
    </tests>
    <help><![CDATA[
    
.. class:: infomark 

==========================
STOC eps for specialists groups
==========================

This tool is an implementation of the gls_adjusted function from `RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
This function adjust the model to account for autocorrelation in the residuals.

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