<?xml version="1.0"?>
<tool id="kraken2_custom_database_builder" name="Kraken2 Custom 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[
        #set $library_list = str($libraries).split(',')
        mkdir kraken2-database && cd kraken2-database &&
        kraken2-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' &&
        #for $library in $library_list:
            #if str($library) != 'None':
                kraken2-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' &&
            #end if
        #end for
        #for $fasta in $input_fasta:
            #if str($fasta) != 'None':
                kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' &&
            #end if
        #end for
        kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
        cd .. &&
        python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
    ]]>
    </command>
    <inputs>
        <param name="database_name" type="text" label="Name for this database" />
        <param name="libraries" type="select" multiple="true" label="Select partial library to download">
            <option value="archaea">Archaea</option>
	    <option value="bacteria">Bacteria</option>
            <option value="plasmid">Plasmid</option>
            <option value="viral">Viral</option>
            <option value="human">Human</option>
        </param>
        <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
        <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>