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view data_manager/kraken2_build_standard.xml @ 0:7e43f66abe9d draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
author dfornika
date Thu, 28 Feb 2019 02:32:38 -0500
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children ce101123d015
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<?xml version="1.0"?>
<tool id="kraken2_build_standard" name="Kraken2 Standard Database Builder (subprocess)" 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_standard.py'
          '${out_file}'
          --threads \${GALAXY_SLOTS:-1}
          --kmer-len ${kmer_len}
          --minimizer-len ${minimizer_len}
          --minimizer-spaces ${minimizer_spaces}
    ]]>
    </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>