<tool id="plot_trend" name="Plot abundance" version="0.1">
    <description>with trend line</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 '$__tool_directory__/plot_trend.R' '$input1' '$input2' '$output' ]]>
    </command>
    <inputs>
        <param format="tabular" name="input1" type="data" label="File generated by the ab_index tool"/>
        <param format="rdata" name="input2" type="data" label="gls model" help="Rdata File"/>
    </inputs>
    <outputs>
        <data format="png" name="output" from_work_dir="output-plot-trend.png" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="data_index.tabular"/>
            <param name="input2" value="gls-adju_rda.rda"/>
            <output name="output" value="trend.png"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark 

==========================
Plot abundance trend 
==========================

This tool is an implementation of the plot_trend function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
This function plot abundance and add a trend line.
    ]]></help>
    <citations>
        <citation type="doi">10.1111/1365-2664.12561</citation>  
    </citations>
</tool>