Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads
annotate 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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899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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1 <tool id="adjust_bracken_kreport_for_unclassified_reads" name="Adjust Kraken-Style Bracken Report for Unclassified Reads" version="0.1.0+galaxy0"> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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2 <description>Adjust kraken-style bracken report to account for unclassified reads</description> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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3 <requirements> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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4 </requirements> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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5 <command detect_errors="exit_code"><![CDATA[ |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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6 '$__tool_directory__/adjust_bracken_kreport_for_unclassified_reads.py' |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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7 --kraken-report '${kraken_report}' |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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8 --kraken-style-bracken-report '${kraken_style_bracken_report}' |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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9 > ${adjusted_report} |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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10 ]]></command> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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11 <inputs> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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12 <param name="kraken_report" type="data" format="txt" /> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
parents:
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13 <param name="kraken_style_bracken_report" type="data" format="txt" /> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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14 </inputs> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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15 <outputs> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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16 <data name="adjusted_report" label="Adjusted Report" format="txt"/> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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17 </outputs> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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18 <tests> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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19 <test> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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20 <param name="kraken_report" value="input/SRR17619849_kraken2.txt"/> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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21 <param name="kraken_style_bracken_report" value=""/> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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22 <output name="adjusted_report" file="" ftype="tabular"/> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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23 </test> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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24 </tests> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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25 <help><![CDATA[ |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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26 ]]></help> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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27 <citations> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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28 </citations> |
899a650587ed
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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29 </tool> |