view data_manager/data_manager_humann2_download.xml @ 3:854d9862a9f1 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee

<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="@VERSION@.0" tool_type="manage_data">
    <description>Download HUMAnN2 database</description>
    <macros>
        <token name="@VERSION@">0.11.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">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>
        python '$__tool_directory__/data_manager_humann2_download.py'
            --database '$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 UniRef90</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 at http://huttenhower.sph.harvard.edu/humann2/manual .
    </help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1003153</citation>
    </citations>
</tool>