Mercurial > repos > iuc > bracken

comparison est-abundance.xml @ 8:1d4bd12f01cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
author iuc
date Thu, 18 Jan 2024 15:38:05 +0000
parents 978ae4147c29
children
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7:978ae4147c29 8:1d4bd12f01cf
31 <options from_data_table="bracken_databases"> 31 <options from_data_table="bracken_databases">
32 <validator message="No database is available" type="no_options"/> 32 <validator message="No database is available" type="no_options"/>
33 </options> 33 </options>
34 </param> 34 </param>
35 <param name="level" type="select" label="Level" help="Level to push all reads to"> 35 <param name="level" type="select" label="Level" help="Level to push all reads to">
36 <option value="S2">Subspecies 2</option>
37 <option value="S1">Subspecies 1</option>
36 <option value="S" selected="true">Species</option> 38 <option value="S" selected="true">Species</option>
37 <option value="G">Genus</option> 39 <option value="G">Genus</option>
38 <option value="F">Family</option> 40 <option value="F">Family</option>
39 <option value="O">Order</option> 41 <option value="O">Order</option>
40 <option value="C">Class</option> 42 <option value="C">Class</option>
72 <param name="logfile_output" value="True"/> 74 <param name="logfile_output" value="True"/>
73 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/> 75 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
74 <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/> 76 <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/>
75 <output name="logfile" file="test2.log" lines_diff="8"/> 77 <output name="logfile" file="test2.log" lines_diff="8"/>
76 </test> 78 </test>
79 <test expect_num_outputs="1">
80 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
81 <param name="level" value="S1"/>
82 <param name="kmer_distr" value="test_entry"/>
83 <param name="logfile_output" value="False"/>
84 <output name="report" file="NC_003198.1_simulated_bracken_report_S1.txt" ftype="tabular"/>
85 </test>
86 <test expect_num_outputs="1">
87 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
88 <param name="level" value="S2"/>
89 <param name="kmer_distr" value="test_entry"/>
90 <param name="logfile_output" value="False"/>
91 <output name="report" file="NC_003198.1_simulated_bracken_report_S2.txt" ftype="tabular"/>
92 </test>
77 </tests> 93 </tests>
78 <help> 94 <help>
79 <![CDATA[ 95 <![CDATA[
80 Bracken relies on Bayesian probabilities that derive from the knowledge about the Kraken classification of each read-length kmer from all genomes within the provided Kraken database. It takes the tabular report output of kraken/kraken2 representing abundance of all detected taxa and provides as output a table representing the re-estimated abundances of different taxa at the taxonomy level pre-determined by the user. For more information about the operation behind the scene, visit http://ccb.jhu.edu/software/bracken/index.shtml?t=manual. 96 Bracken relies on Bayesian probabilities that derive from the knowledge about the Kraken classification of each read-length kmer from all genomes within the provided Kraken database. It takes the tabular report output of kraken/kraken2 representing abundance of all detected taxa and provides as output a table representing the re-estimated abundances of different taxa at the taxonomy level pre-determined by the user. For more information about the operation behind the scene, visit http://ccb.jhu.edu/software/bracken/index.shtml?t=manual.
81 97