<tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
    <description></description>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement>
    </requirements>
    <macros>
        <token name="@TOOL_VERSION@">4.0.6</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <stdio>
        <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/>
        <exit_code range="1:" level="fatal" description="Error"/>
    </stdio>
    <command><![CDATA[
python '$__tool_directory__/data_manager_metaphlan_download.py'
    --index '$index'
    --json '$out_file'
    ]]></command>
    <inputs>
        <param name="index" type="select" label="Version">
            <option value="mpa_vOct22_CHOCOPhlAnSGB_202212" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202212</option>
            <option value="mpa_vJan21_CHOCOPhlAnSGB_202103">FULL: mpa_vJan21_CHOCOPhlAnSGB_202103</option>
            <option value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103">DEMO: mpa_vJan21_TOY_CHOCOPhlAnSGB_202103</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
                    <has_text text="MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tool downloads and builds the MetaPhlAn databases.
    ]]></help>
    <citations>
        <citation type="doi">1101/2020.11.19.388223</citation>
        <yield />
    </citations>
</tool>