<commit_before><macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.18.0">gemini</requirement>
            <requirement type="package" version="0.1.3">grabix</requirement>
            <requirement type="package" version="0.2.6">tabix</requirement>
            <requirement type="package" version="0.1.19">samtools</requirement>
            <requirement type="package" version="2.19.1">bedtools</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>gemini --version</version_command>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>

    <xml name="annotation_dir">
        <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
            <options from_data_table="gemini_databases">
                <filter type="sort_by" column="0" />
                <validator type="no_options" message="No annotation database is available" />
            </options>
        </param><commit_msg>The dependencies are part of the installation.<commit_after><macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.18.0">gemini</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>gemini --version</version_command>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>

    <xml name="annotation_dir">
        <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
            <options from_data_table="gemini_databases">
                <filter type="sort_by" column="0" />
                <validator type="no_options" message="No annotation database is available" />
            </options>
        </param>
{'fraction_non_alphanumeric': 0.14759309718437782, 'fraction_numerical': 0.012715712988192553, 'mean_word_length': 2.2979041916167664, 'pattern_counts': {'":': 2, '<': 65, '<?xml version=': 0, '>': 65, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 14}, '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': '2111614', 'n_tokens_mistral': 635, 'n_tokens_neox': 608, 'n_words': 121}