<?xml version="1.0"?>
<tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.0">
    <description>database builder</description>
    <requirements>
        <requirement type="package" version="0.10.5">kraken</requirement>
        <requirement type="package" version="1.1.11">jellyfish</requirement>
        <requirement type="set_environment">KRAKEN_SCRIPT_PATH</requirement>
    </requirements>
    <stdio>
        <exit_code description="Error" level="fatal" range="1:" />
    </stdio>
    <version_command>kraken -version | awk '{print $NF}'</version_command>
    <command>
    <![CDATA[
        #set $library_list = str($libraries).split(',')
        mkdir kraken-database && cd kraken-database &&
        kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" &&
        #for $library in $library_list:
            kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}"  &&
        #end for
        #for $fasta in $input_fasta:
            kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta"  &&
        #end for
        kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len}  &&
        cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}"
    ]]>
    </command>
    <inputs>
        <param label="Name for this database" name="database_name" type="text" />
        <param label="Select partial library to download" multiple="True" name="libraries" type="select">
            <option value="bacteria">Bacteria</option>
            <option value="plasmids">Plasmids</option>
            <option value="viruses">Viruses</option>
            <option value="human">Human</option>
        </param>
        <param format="fasta" label="Select history item" multiple="True" name="input_fasta" optional="True" type="data" />
        <param label="K-mer length in BP" name="kmer_len" type="integer" value="31" />
        <param label="Minimizer length" name="minimizer_len" type="integer" value="15" />
    </inputs>
    <outputs>
        <data format="data_manager_json" name="out_file" />
    </outputs>
    <citations>
        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
    </citations>
</tool>