<commit_before><tool id="humann" name="Functional profiling">

    <description>with HUMAnN</description>

    <macros>
    </macros>

    <requirements>
    </requirements>

    <stdio>
        <regex match="error"
               source="stderr"
               level="fatal"
               description="" />
        <regex match="warning"
               source="stderr"
               level="warning"
               description="" />
    </stdio>

    <version_command></version_command>

    <!--<command>-->
    <command interpreter="python">
        humann_wrapper.py
            --input=$input_file
            --report=$report_file
            #set humann_dir=os.getcwd()+"/tools/analyze_metabolism/humann/humann/"
            --humann_dir=$humann_dir
            --cog_extracted_data=$cog_use
<commit_msg>Comment error in stdio for humann wrapper<commit_after><tool id="humann" name="Functional profiling">

    <description>with HUMAnN</description>

    <macros>
    </macros>

    <requirements>
    </requirements>

    <stdio>
        <regex match="error"
               source="stderr"
               level="fatal"
               description="" />
        <regex match="warning"
               source="stderr"
               level="warning"
               description="" />
        <!--<regex match="not found"
               source="stderr"
               level="fatal"
               description="" />-->
    </stdio>

    <version_command></version_command>

    <!--<command>-->
    <command interpreter="python">
        humann_wrapper.py
            --input=$input_file
            --report=$report_file
            #set humann_dir=os.getcwd()+"/tools/analyze_metabolism/humann/humann/"
            --humann_dir=$humann_dir
            --cog_extracted_data=$cog_use

{'fraction_non_alphanumeric': 0.13557422969187674, 'fraction_numerical': 0.0, 'mean_word_length': 1.8170347003154574, 'pattern_counts': {'":': 0, '<': 37, '<?xml version=': 0, '>': 37, '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': '4935168', 'n_tokens_mistral': 516, 'n_tokens_neox': 488, 'n_words': 78}