<tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0">
    <description>Extract intervals not represented by an interval file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        complementBed
        -i "$input"
        -g "$genome"
        > "$output"
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
        <expand macro="genome" />
    </inputs>
    <outputs>
        <data format_source="input" name="output" metadata_source="input" label="Complemen of ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="a.bed" ftype="bed" />
            <param name="genome" value="mm9_chr1.len" />
            <output name="output" file="complementBed_result1.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.

.. image:: $PATH_TO_IMAGES/complement-glyph.png

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