<commit_before><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><commit_msg>Fix some spacing in the help section.<commit_after><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>
{'fraction_non_alphanumeric': 0.14745916515426497, 'fraction_numerical': 0.019056261343012703, 'mean_word_length': 2.4027777777777777, 'pattern_counts': {'":': 2, '<': 47, '<?xml version=': 0, '>': 47, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 8}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6043457', 'n_tokens_mistral': 702, 'n_tokens_neox': 651, 'n_words': 179}