<tool id="regionalgam_autocor_acf" name="Autocorrelation test" version="@VERSION@">
    <description>check for temporal autocorrelation in the residuals</description>
    <macros>
        <import>regionalgam_macros.xml</import>
    </macros>
    <expand macro="rg_r_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/autocorr-res-acf.R'
            '$gls_model' 
            '$output' 
            '$output_res_values' 
    ]]>
    </command>
    <inputs>
        <expand macro="rg_gls_model"/>
    </inputs>
    <outputs>
        <data format="png" name="output" from_work_dir="output-acf.png" />
        <data format="txt" name="output_res_values" from_work_dir="output-acf.txt" />
    </outputs>
    <tests>
        <test>
            <param name="gls_model" value="s_gls_rda.rda"/>
            <output name="output_res_values" file="s_res.txt"/>
        </test>
    </tests>

    <help><![CDATA[
======================================
Model residuals autocorrelation check 
======================================

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

This function uses a simple linear model and explore for temporal autocorrelation that we will account in the final model.

Use a gls model and visualize autocorrelation in the residuals with the png output file.

|

**Outputs**

The tools returns residuals visualization in an image png file, and raw values in a text file.

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