<macros>
    <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">mummer4</xref>
        </xrefs>
    </xml>
    <xml name="citation">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1005944</citation>
        </citations>
    </xml>
    <token name="@TOOL_VERSION@">4.0.0rc1</token>
    <token name="@VERSION_SUFFIX@">3</token>
    <token name="@PROFILE@">20.05</token>
    <xml name="gnuplot_requirement">
        <requirement type="package" version="5.4.8">gnuplot</requirement>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
            <requirement type="package" version="1.19.2">samtools</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="mumplot_input" >
        <yield />
        <param name="breaklen" type="integer" argument="-b" value="20" label="Break Length"
            help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" />
        <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." >
            <option value="">Color</option>
            <option value="-color">No color (-color)</option>
        </param>
        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the default dotplot." >
            <option value="">Dotplot</option>
            <option value="-c">Coverage Plot (-c)</option>
        </param>
        <param type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
            help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" />
        <param type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
        <conditional name="labels" >
            <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
                <option value="no">NO</option>
                <option value="yes">YES</option>
            </param>
            <when value="yes" >
                <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" />
                <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" />
            </when>
            <when value="no" />
        </conditional>
        <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" >
            <option value="small">Small</option>
            <option value="medium">Medium</option>
            <option value="large">Large</option>
        </param>
        <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
        <param type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
        <conditional name="range" >
            <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
                <option value="no">NO</option>
                <option value="yes">YES</option>
            </param>
            <when value="yes" >
                <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" />
                <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" />
                <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" />
                <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" />
            </when>
            <when value="no" />
        </conditional>
    </xml>
</macros>