Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads

<tool id="adjust_bracken_for_unclassified_reads" name="Adjust Bracken Report for Unclassified Reads" version="0.1.0">
    <description>Adjust bracken report to account for unclassified reads</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        '$__tool_directory__/adjust_bracken_for_unclassified_reads.py'
        --kraken-report '${kraken_report}'
        --bracken-abundances '${bracken_abundances}'
        > ${adjusted_bracken_report}
    ]]></command>
    <inputs>
        <param name="kraken_report" type="data" format="txt" />
        <param name="bracken_abundances" type="data" format="txt" />
    </inputs>
    <outputs>
        <data name="adjusted_bracken_report" label="Adjusted Report" format="txt"/>
    </outputs>
    <tests>
        <test>
            <param name="kraken_report" value="input/SRR17619849_kraken2.txt"/>
            <param name="bracken_abundances" value="input/SRR17619849_bracken_abundances.tsv"/>
            <output name="adjusted_bracken_report" file="output/SRR17619849_bracken_abundances_adjusted.tsv" ftype="tabular"/>
        </test>
        <test>
            <param name="kraken_report" value="input/SRR17907745_kraken2.txt"/>
            <param name="bracken_abundances" value="input/SRR17907745_bracken_abundances.tsv"/>
            <output name="adjusted_bracken_report" file="output/SRR17907745_bracken_abundances_adjusted.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>
author	public-health-bioinformatics
date	Thu, 10 Mar 2022 21:35:14 +0000
parents
children	3cde438eb222