<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>
        macs2 filterdup
            -i "${ infile }"
            -o temp_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 "${ keep_dup_options.keep_dup_options_selector }"
        #end if
	;
	mv temp_outfile "${ outfile }"
    </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>
**What it does**

Remove duplicate reads at the same position, then convert acceptable format to BED format.
filterdup tool from macs2

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