<commit_before><tool id="picrust_metagenome_contributions" name="Metagenome Contributions" version="@WRAPPER_VERSION@.0">
    <description>of OTUs to user-specified functions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        metagenome_contributions.py
            -i '$input_data'
            -o '$contrib_table'
            -c '$gg.precalc'
            -l '$limit_gene'
    ]]></command>
    <inputs>
        <param name="input_data" type="data" format="biom1" label="Input file" help="Biom file, which should be the output of the normalize_by_copy_number command."/>
        <expand macro="otu-reference-precalculated"/>
        <param name="limit_gene" type="text" format="txt" label="Function ids" help="Limit to specified function ids (e.g. K00500). If limiting to multiple ids then separate them by commas with no spaces between them." />
    </inputs>
    <outputs>
        <data name="contrib_table" format="tabular">
    </outputs>
    <tests>
        <test>
            <param name="input_data" value="otu_table_for_custom_trait_table.biom"/>
            <param name="source" value="hist"/>
            <param name="precalc" value="custom_trait_table.tab"/>
            <output name="precalc" ftype="txt">
                <assert_contents>
                    <has_text text="GeneCountPerGenome"/>
                    <has_text text="OTUAbundanceInSample"/>
                </assert_contents>
            </output>
        </test>
    </tests><commit_msg>fixed typo in output name<commit_after><tool id="picrust_metagenome_contributions" name="Metagenome Contributions" version="@WRAPPER_VERSION@.0">
    <description>of OTUs to user-specified functions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        metagenome_contributions.py
            -i '$input_data'
            -o '$contrib_table'
            -c '$gg.precalc'
            -l '$limit_gene'
    ]]></command>
    <inputs>
        <param name="input_data" type="data" format="biom1" label="Input file" help="Biom file, which should be the output of the normalize_by_copy_number command."/>
        <expand macro="otu-reference-precalculated"/>
        <param name="limit_gene" type="text" format="txt" label="Function ids" help="Limit to specified function ids (e.g. K00500). If limiting to multiple ids then separate them by commas with no spaces between them." />
    </inputs>
    <outputs>
        <data name="contrib_table" format="tabular">
    </outputs>
    <tests>
        <test>
            <param name="input_data" value="otu_table_for_custom_trait_table.biom"/>
            <param name="source" value="hist"/>
            <param name="precalc" value="custom_trait_table.tab"/>
            <output name="contrib_table" ftype="txt">
                <assert_contents>
                    <has_text text="GeneCountPerGenome"/>
                    <has_text text="OTUAbundanceInSample"/>
                </assert_contents>
            </output>
        </test>
    </tests>
{'fraction_non_alphanumeric': 0.13227189222290264, 'fraction_numerical': 0.004286589099816289, 'mean_word_length': 2.6915254237288138, 'pattern_counts': {'":': 0, '<': 69, '<?xml version=': 0, '>': 69, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, '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': '4031329', 'n_tokens_mistral': 970, 'n_tokens_neox': 929, 'n_words': 215}