<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>Extract intervals not represented by an interval file</description>
    <expand macro="bio_tools" />
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
complementBed
-i '$input'
-g @GENOME_FILE@
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <expand macro="input_conditional_genome_file" />
    </inputs>
    <outputs>
        <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="a.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <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 @STD_BEDTOOLS_INPUT_LABEL@ file.

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

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