<tool id="gops_complement_1" name="Complement" version="1.0.0">
    <description>intervals of a dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <code file="operation_filter.py"/>
    <command><![CDATA[
python '$__tool_directory__/gops_complement.py'
'$input1'
'$output'
-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
-l '${chromInfo}'
$allchroms
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="interval" label="Complement regions of" />
        <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement" />
    </inputs>
    <outputs>
        <data name="output" format_source="input1" metadata_source="input1" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="1.bed" dbkey="hg17" />
            <param name="allchroms" value="true" />
            <output name="output" file="gops_complement_out.bed" />
        </test>
        <test>
            <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
            <param name="allchroms" value="true" />
            <output name="output" file="gops_complement_out_diffCols.dat" />
        </test>
        <test>
            <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
            <param name="allchroms" value="true" />
            <output name="output" file="gops_complement_out2.bed" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.

This operation complements the regions of a set of intervals.  Regions are returned that represent the empty space in the input interval.

@SCREENCASTS@

**Syntax**

- **Genome-wide complement** will complement all chromosomes of the genome.  Leaving this option unchecked will only complement chromosomes present in the dataset.

-----

**Example**

.. image:: gops_complement.gif
    ]]></help>
</tool>