view humann2_split_table.xml @ 0:36a78e81ee4c draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty

<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="stdio"/>

    <version_command>
<![CDATA[
    humann2_split_table --version
]]>
    </version_command>

    <command><![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,biom" 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[
**What it does**

HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.

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>