<?xml version="1.0"?>
<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.4" profile="23.0">
    <description>taxonomy downloader</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/data_manager.py' --out '${out_file}'
        #if $taxonomy_url:
            --url '${taxonomy_url}'
        #end if
        #if $database_name:
            --name '${database_name}'
        #end if
        $name_maps
        $partial_data
    ]]>
    </command>
    <inputs>
        <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
        <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" />
        <param name="name_maps" type="boolean" truevalue="--name-maps" falsevalue="" label="Also download accession2taxid data" checked="false" />
        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <param name="database_name" value="tax_name"/>
            <output name="out_file" value="taxonomy.json"/>
        </test>
        <test>
            <param name="database_name" value="tax_name"/>
            <param name="name_maps" value="true"/>
            <param name="partial_data" value="--partial"/>
            <output name="out_file" value="taxonomy_with_accession2taxid.json"/>
        </test>
    </tests>
    <help>
        Download a taxonomy dump from a provided URL.
        The default URL is the latest dump from NCBI taxonomy.
        The accession2taxid data comes from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ and can be used by the Diamond data_manager (uses ~20Gb as of 2021).
    </help>
</tool>