<?xml version="1.0"?>
<tool id="kraken2_build_special" name="Kraken2 Special Database Builder" tool_type="manage_data" version="2.0.7_beta">
    <description>database builder</description>
    <requirements>
        <requirement type="package" version="2.0.7_beta">kraken2</requirement>
    </requirements>
    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/kraken2_build_special.py'
          '${out_file}'
	  --db-type ${db_type}
          --threads \${GALAXY_SLOTS:-1}
          --kmer-len ${kmer_len}
          --minimizer-len ${minimizer_len}
          --minimizer-spaces ${minimizer_spaces}
    ]]>
    </command>
    <inputs>
        <param name="db_type" type="select" multiple="false" label="Select database to build">
            <option value="greengenes">Greengenes</option>
	    <option value="silva">Silva</option>
	    <option value="rdp">RDP</option>
        </param>
        <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
        <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
	<param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>
    </help>
    <citations>
        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
    </citations>
</tool>