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planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
author public-health-bioinformatics
date Thu, 27 Oct 2022 19:13:25 +0000
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<tool id="adjust_bracken_kreport_for_unclassified_reads" name="Adjust Kraken-Style Bracken Report for Unclassified Reads" version="0.1.0+galaxy0">
    <description>Adjust kraken-style bracken report to account for unclassified reads</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        '$__tool_directory__/adjust_bracken_kreport_for_unclassified_reads.py'
        --kraken-report '${kraken_report}'
        --kraken-style-bracken-report '${kraken_style_bracken_report}'
        > ${adjusted_report}
    ]]></command>
    <inputs>
        <param name="kraken_report" type="data" format="txt" />
        <param name="kraken_style_bracken_report" type="data" format="txt" />
    </inputs>
    <outputs>
        <data name="adjusted_report" label="Adjusted Report" format="txt"/>
    </outputs>
    <tests>
        <test>
            <param name="kraken_report" value="input/SRR17619849_kraken2.txt"/>
            <param name="kraken_style_bracken_report" value=""/>
            <output name="adjusted_report" file="" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>