<commit_before><tool id="tb_profiler_vcf_profile" name="TB-Profiler VCF-Profile" version="2.5">
    <description>Infer strain types and drug resistance markers from sequences</description>
    <requirements>
        <requirement type="package" version="2.5">tb-profiler</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$vcf_input' input.vcf.gz &&
        
        tb-profiler vcf_profile input.vcf.gz           
        
        #if $output_format == "csv"
            --csv
        #else if $output_format == "txt"
            --txt
        #end if<commit_msg>added the updatedb line<commit_after><tool id="tb_profiler_vcf_profile" name="TB-Profiler VCF-Profile" version="2.5">
    <description>Infer strain types and drug resistance markers from sequences</description>
    <requirements>
        <requirement type="package" version="2.5">tb-profiler</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$vcf_input' input.vcf.gz &&

        tb-profiler update_tbdb &&
        
        tb-profiler vcf_profile input.vcf.gz           
        
        #if $output_format == "csv"
            --csv
        #else if $output_format == "txt"
            --txt
        #end if
{'fraction_non_alphanumeric': 0.1240126382306477, 'fraction_numerical': 0.00631911532385466, 'mean_word_length': 2.4336043360433606, 'pattern_counts': {'":': 0, '<': 21, '<?xml version=': 0, '>': 19, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, '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': '7141536', 'n_tokens_mistral': 391, 'n_tokens_neox': 390, 'n_words': 82}