<tool id="plot_coverage" name="Plot coverage" version="0.5.2">
    <description>as area plot between BAM files</description>
    <requirements>
        <requirement type="package" version="0.5.2">readtagger</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        #import re
        #set identifier1 = re.sub('[^\w\-_\.\,]', '_', str( $input1.element_identifier))
        #set identifier2 = re.sub('[^\w\-_\.\,]', '_', str( $input2.element_identifier))
        plot_coverage '$input1' '$identifier1' '$input2' '$identifier2' output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="bam,cram" label="Select a BAM file to plot"/>
        <param name="input2" type="data" format="bam,cram" label="Select a second BAM file to plot" optional="true"/>
        <param name="regions" type="text" label="Select regions to plot" optional="true" help="e.g X:1200000-1250000,X1250000-1300000. If left blank will plot all contigs/chromosomes.">
            <sanitizer>
                <valid initial="string.letters,string.digits">
                    <add value="-" />
                    <add value="," />
                    <add value=":" />
                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="three_cluster_out.bam" ftype="bam"/>
            <param name="input2" value="three_cluster_out.bam" ftype="bam"/>
            <param name="regions" value="3R:13373525-13373615"/>
            <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

This tool plots the coverage over a specified region (by default all chromosomes/contigs).

    ]]></help>
</tool>