<commit_before><?xml version="1.0"?>
<tool id="kraken2_build_custom" 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 $NF}'</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/kraken2_build_custom.py'
          '${out_file}'
          --threads \${GALAXY_SLOTS:-1}
          --db ${database_name}
          --kmer-len ${kmer_len}
          --minimizer-len ${minimizer_len}
          --minimizer-spaces ${minimizer_spaces}
          --fasta ${input_fasta}
    ]]>
    </command>
    <inputs>
        <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
	<param name="database_name" type="text" label="Name for this database" />
        <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>
<commit_msg>Quote db path in tool wrapper<commit_after><?xml version="1.0"?>
<tool id="kraken2_build_custom" 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 $NF}'</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/kraken2_build_custom.py'
          '${out_file}'
          --threads \${GALAXY_SLOTS:-1}
          --db '${database_name}'
          --kmer-len ${kmer_len}
          --minimizer-len ${minimizer_len}
          --minimizer-spaces ${minimizer_spaces}
          --fasta ${input_fasta}
    ]]>
    </command>
    <inputs>
        <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
	<param name="database_name" type="text" label="Name for this database" />
        <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>

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