<tool id="autocor-acf" name="Autocorrelation test" version="0.1">
    <description>check for temporal 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>
        <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
        <requirement type="package" version="1.1.2">xorg-libsm</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/autocorr-res_acf.R' '$input1' '$output' ]]>
    </command>
    <inputs>
        <param format="rdata" name="input1" type="data" label="gls model" help="Rdata file"/>
    </inputs>
    <outputs>
        <data format="png" name="output" from_work_dir="output-acf.png" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="mod1"/>
            <param output="output" value="res.png"/>
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark 

======================================
Model residuals autocorrelation check 
/bin/bash: :wq: command not found

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