<tool id="humann2_split_table" name="Split" version="@WRAPPER_VERSION@.0">
    <description> a HUMAnN2 generated table</description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann2_split_table
    --input '$input'
    -o 'output'
    #if $taxonomy_index
        --taxonomy_index '$taxonomy_index'
    #end if
    #if $taxonomy_level
        --taxonomy_level '$taxonomy_level'
    #end if
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular,biom1" label="Gene table to split"/>
        <param argument="--taxonomy_index" type="text" label="Index of the gene in the taxonomy data" optional="true"/>
        <param argument="--taxonomy_level" type="select" label="Level of taxonomy for the output" optional="true" help="if input is from picrust metagenome_contributions.py">
            <option value="Kingdom">Kingdom</option>
            <option value="Phylum">Phylum</option>
            <option value="Class">Class</option>
            <option value="Order">Order</option>
            <option value="Family">Family</option>
            <option value="Genus">Genus</option>
            <option value="Species">Species</option>
        </param>
    </inputs>
    <outputs>
        <collection type="list" name="split_tables" label="${tool.name} on ${on_string}: Split tables">
            <discover_datasets pattern="__designation_and_ext__" directory="output"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="joined_pathway_coverage_abundance.tsv"/>
            <output_collection name="split_tables" type="list" >
                <element name="demo_Coverage" file="demo_Coverage.tsv" />
                <element name="demo_Abundance" file="demo_Abundance.tsv" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Split HUMAnN2 table is a tool to split a gene table with multiple columns. This file can have been generated with the join table tool.
    ]]></help>
    <expand macro="citations"/>
</tool>
