<tool id="kmer2stats" name="Kmer2Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
    <description>A tool that computes kmer alpha diversity metrics and other statistics</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">kmer2stats</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
        kmer2stats.py 
        '$input_file'
        &&
        cp 'compute_diversity.csv' '$output_file'
    ]]>
    </command>
    <inputs>
        <param name="input_file" type="data" format="tabular,txt" label="File input"/> 
    </inputs>
    <outputs>
        <data name="output_file" format="tabular" label="${tool.name}: kmer statistics"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_file" ftype="txt" value="test_file.txt"/>
            <output name="output_file" ftype="tabular" value="compute_diversity.csv"/>
        </test>
    </tests>
    <help>
    <![CDATA[

        **What this tool does**

        This tool calculates alpha diversity metrics and other statistics such as observed features based on counted kmers.

        **Input**

        This tool was designed to use the output from jellyfish but it also can take any file that looks like this:

        ::

         ANYTHING SINCE THIS LINE WILL ALWAYS BE SKIPPED
         AAAAAA 8453
         AAAAAC 6870
         AAAAAG 6312
         AAAAAT 7966
         AAAACA 5133
         AAAACC 5600
         AAAACG 5870
         AAAACT 3911
         AAAAGA 4173
         AAAAGC 5078
         AAAAGG 3047
         AAAAGT 3067
         AAAATA 5726
         AAAATC 6167
         AAAATG 5731
         AAAATT 4987
         AAACAA 3719
         AAACAC 2817
         AAACAG 5565

        The first line will always be skipped so be sure to start the counted kmers in the second row!

        **Output**

        Two column table with metric name in the first column and value in second column.

        ::

         Metric	Value
         shannon	3.0008343481203097
         simpson_d	0.05166872360281036
         pielou_e	0.9856502651904311

    ]]>
    </help>
    <citations>
        <citation type="bibtex">@misc{BibEntry2025Apr,
            title = {{kmer2stats}},
            author = {Santino Faack (SantaMcCloud)},
            journal = {GitHub},
            year = {2025},
            month = apr,
            url = {https://github.com/SantaMcCloud/kmer2stats}
        }</citation>
    </citations>
</tool>