<tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0">
    <description>Call peaks from bedGraph output</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 bdgpeakcall
        --ifile '${ infile }'
        --cutoff '${ cutoff }'
        --min-length '${ minlen }'
        --max-gap '${ maxgap }'
        ${ cutoff_analysis } 
        ${ notrackline }
        --ofile '${ outfile }'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
        <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
            help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5.0 (--cutoff)"/>
        <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value. Default=200 (--min-length)"/>
        <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size Default=30 (--max-gap)"/>
        <param name="cutoff_analysis" type="boolean" truevalue="--cutoff-analysis" falsevalue="" checked="False" label="Perform cutoff analysis" help="While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, --min-len and --max-gap may affect the results. Default=False (--cutoff-analysis)"/>
        <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" label="Include trackline into bedGraph output" help="required by UCSC Genome Browser (--no-trackline)"/>
    </inputs>
    <outputs>
        <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" />
            <param name="cutoff" value="5.0"/>
            <param name="minlen" value="200"/>
            <param name="maxgap" value="30"/>
            <output name="outfile">
                <assert_contents>
                    <has_text text="chrV" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" />
            <param name="cutoff" value="5.0"/>
            <param name="minlen" value="200"/>
            <param name="maxgap" value="30"/>
            <param name="cutoff_analysis" value="true" />
            <output name="outfile" file="bdgpeakcall_output_cutoff.bdg"/>
        </test>
    </tests>
    <help>
    <![CDATA[
**What it does**

This is **bdgpeakcall** utility from the MACS2_ Package. It calls peaks from bedGraph output.

.. _MACS2: https://github.com/taoliu/MACS


@citation@
    ]]>
    </help>
    <expand macro="citations" />
</tool>