<macros>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.19.1">bedtools</requirement>
        </requirements>
        <version_command>bedtools --version</version_command>
    </xml>
    <token name="@REFERENCES@">
------

This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__.
If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__

    .. __: https://github.com/arq5x/bedtools2
    .. __: http://cphg.virginia.edu/quinlan/
    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
    </token>
</macros>

<macros>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.19.1">bedtools</requirement>
        </requirements>
        <version_command>bedtools --version</version_command>
    </xml>
    <token name="@REFERENCES@">
------

This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__.
If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__

.. __: https://github.com/arq5x/bedtools2
.. __: http://cphg.virginia.edu/quinlan/
.. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
    </token>
</macros>

Fix some spacing in the help section.
Fix some spacing in the help section.
