<tool id="regionalgam_gls_adjusted" name="Linear regression ajusted" version="@VERSION@">
    <description>for autocorrelation in the residuals</description>
    <macros>
        <import>regionalgam_macros.xml</import>
    </macros>
    <expand macro="rg_nlme_mass_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/gls-adjusted.R'
            '$collated_index' '$ab_indices' 
            '$output' '$output2'
    ]]>
    </command>
    <inputs>
        <expand macro="rg_collated_index"/>
        <expand macro="rg_ab_indices"/>
    </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>
            <param name="collated_index" value="s_glmmpql.tabular"/>
            <param name="ab_indices" value="s_data_index.tabular"/>
            <output name="output" file="s_gls-adju_sum.txt"/>
            <output name="output2" file="s_gls-adju_rda.rda" compare="sim_size" delta="100"/>
        </test>
    </tests>
    <help><![CDATA[
==========================
Linear regression ajusted
==========================

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.

|

**Outputs**

The tool returns the linear regression model in an Rdata file.

It also returns a summary of this model in txt format.

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