<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="0.9.9" tool_type="manage_data">
    <description>Download HUMAnN2 database</description>
    <requirements>
        <requirement type="package" version="0.9.9">humann2</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
    <command interpreter="python">
        data_manager_humann2_download.py
            --database '$db.database'
            --build '$db.build'
            '${out_file}'
    </command>
    <inputs>
        <conditional name="db">
            <param name="database" type="select" label="Type of database to download">
                <option value="chocophlan" selected="true">Nucleotide database</option>
                <option value="uniref">Protein database</option>
            </param>
            <when value="chocophlan">
                <param name="build" type="select" label="Build for nucleotide database">
                    <option value="full" selected="true">Full</option>
                    <option value="DEMO">Demo</option>
                </param>
            </when>
            <when value="uniref">
                <param name="build" type="select" label="Build for protein database">
                    <option value="uniref50_diamond">Full UniRef50</option>
                    <option value="uniref50_ec_filtered_diamond">EC-filtered UniRef50</option>
                    <option value="uniref50_GO_filtered_rapsearch2">GO filtered UniRef50 for rapsearch2</option>
                    <option value="uniref90_diamond" selected="true">Full UniRef50</option>
                    <option value="uniref90_ec_filtered_diamond">EC-filtered UniRef90</option>
                    <option value="DEMO_diamond">Demo</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
    </tests>
    <help>

This tool downloads the HUMAnN2 databases.

`Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.

    </help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1003153</citation>
        <yield />
    </citations>
</tool>