<?xml version="1.0"?>
<tool id="kraken2_standard_database_builder" name="Kraken2 Standard 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 $NF}'</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        #import datetime
	#set kraken2_db_name = datetime.date.today().strftime('%Y-%m-%d') + "_standard"
        mkdir kraken2-database && cd kraken2-database &&
        kraken2-build 
          --standard
	  --threads \${GALAXY_SLOTS:-1}
          --db '${kraken2_db_name}'
          --kmer-len ${kmer_len}
          --minimizer-len ${minimizer_len}
          --minimizer-spaces ${minimizer_spaces} &&
        cd .. &&
        python '$__tool_directory__/make_json.py' --db '${kraken2_db_name}' --out '${out_file}'
    ]]>
    </command>
    <inputs>
        <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>