view humann2_split_table.xml @ 0:3d6f37e7e3a8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

<tool id="humann2_split_table" name="Split" version="0.6.1">
    <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
            -i $input_file
            -o "output"
    ]]></command>

    <inputs>
        <param name="input_file" type="data" format="tsv,biom" label="Table to split into multiple tables" help="(-i)"/>
    </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_file" value="joined_pathway_coverage_abundance.tsv"/>
            <output_collection name="split_tables" type="list" >
                <element name="humann2_Abundance" file="split_joined_table_abundances.tsv" />
                <element name="humann2_Coverage" file="split_joined_table_coverage.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 table with multiple columns. This file can have been generated with the join table tool.
    ]]></help>

    <expand macro="citations"/>
</tool>