<tool id="humann_reduce_table" name="Reduce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>a joined HUMAnN table</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann_reduce_table
    --input '$input'
    -o '$output'
    --function '$function'
    --sort-by '$sort_by'
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway/taxonomic table"/>
        <param argument="--function" type="select" label="Function to apply to select value to keep">
            <option value="max" selected="true">Max</option>
            <option value="sum">Sum</option>
            <option value="mean">Mean</option>
            <option value="min">Min</option>
        </param>
        <param argument="--sort-by" type="select" label="How to sort the output">
            <option value="name" selected="true">Name</option>
            <option value="value">Value</option>
            <option value="level">Level</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="demo_joined_pathabundance_pathcoverage.tsv"/>
            <param name="function" value="max"/>
            <param name="sort_by" value="name"/>
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_text text="max" />
                    <has_text text="UNINTEGRATED|unclassified" />
                    <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This tool reduces a joined HUMAnN table. It selects for each row which value to keep given a function (max, sum, mean or min).
    ]]></help>
    <expand macro="citations"/>
</tool>