Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads
diff adjust_bracken_kreport_for_unclassified_reads.xml @ 3:899a650587ed draft default tip
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 |
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date | Thu, 27 Oct 2022 19:13:25 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/adjust_bracken_kreport_for_unclassified_reads.xml Thu Oct 27 19:13:25 2022 +0000 @@ -0,0 +1,29 @@ +<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>