annotate humann2_reduce_table.xml @ 3:1c802bbbed99 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908"

<tool id="humann2_reduce_table" name="Reduce" 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_reduce_table
    --input '$input'
    -o '$output_table'
    --function '$function'
    --sort-by '$sort'
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
        <param argument="--function" type="select" label="Function to apply">
            <option value="max" selected="true">Max</option>
            <option value="sum">Sum</option>
            <option value="mean">Mean</option>
            <option value="min">Min</option>
        </param>
        <param name="sort" type="select" label="How to sort the output" argument="--sort-by">
            <option value="name" selected="true">Name</option>
            <option value="value">value</option>
            <option value="level">level</option>
        </param>
    </inputs>
    <outputs>
        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Reduced table" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="demo_genefamilies.tsv"/>
            <param name="function" value="max"/>
            <param name="sort" value="name"/>
            <output name="output_table" file="max_reduced_gene_family_abundance.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Reduce HUMAnN2 table is a tool to reduce the table given a function (max, sum, mean or min).
    ]]></help>
    <expand macro="citations"/>
</tool>