<tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.0">
    <description>Remove duplicate reads at the same position</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 filterdup
            -i '${ infile }'
            -o '${ outfile }'
        --format '${ infile.extension.upper() }'
        @effective_genome_size@
        @tag_size@
        --pvalue '${ pvalue }'
        #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
            --keep-dup '${ keep_dup_options.user_keepdup }'
        #else
            --keep-dup '${ keep_dup_options.keep_dup_options_selector }'
        #end if
    ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
        <expand macro="conditional_effective_genome_size" />
        <expand macro="tag_size" />
        <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" />
        <expand macro="keep_duplicates" />

    </inputs>
    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/>
            <param name="pvalue" value="1e-5"/>
            <param name="keep_dup_options_selector" value="auto"/>
            <param name="effective_genome_size_options_selector" value="user_defined" />
            <param name="gsize" value="3300000000" />
            <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format.

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

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