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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 73af464cc860250c3fa3dd433602283ab5a44f53-dirty
author pimarin
date Thu, 22 Dec 2022 15:01:43 +0000
parents ca9e2125c5de
children 44fb905481f0
comparison
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2:ca9e2125c5de 3:eea334d9988b
1 <?xml version="1.0"?> 1
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.4.2</token> 3 <token name="@TOOL_VERSION@">1.6.1</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@BAKTA_VERSION@">1.5</token>
5 <token name="@PROFILE@">21.05</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 <xml name="version_command"> 6 <token name="@PROFILE@">21.05</token>
7 <version_command><![CDATA[bakta --version]]></version_command> 7 <xml name="version_command">
8 </xml> 8 <version_command><![CDATA[bakta --version]]></version_command>
9 <xml name="edam">
10 <edam_topics>
11 <edam_topic>topic_3174</edam_topic>
12 </edam_topics>
13 </xml> 9 </xml>
14 <xml name="xrefs"> 10 <xml name="edam">
15 <xrefs> 11 <edam_topics>
16 <xref type='bio.tools'>Bakta</xref> 12 <edam_topic>topic_3174</edam_topic>
17 </xrefs> 13 </edam_topics>
18 </xml> 14 </xml>
19 <xml name="requirements"> 15 <xml name="xrefs">
20 <requirements> 16 <xrefs>
21 <requirement type="package" version="@TOOL_VERSION@">bakta</requirement> 17 <xref type='bio.tools'>Bakta</xref>
22 </requirements> 18 </xrefs>
23 </xml> 19 </xml>
24 <xml name="citations"> 20 <xml name="requirements">
25 <citations> 21 <requirements>
26 <citation type="bibtex"> 22 <requirement type="package" version="@TOOL_VERSION@">bakta</requirement>
27 @article{mbs:/content/journal/mgen/10.1099/mgen.0.000685, 23 </requirements>
28 author = "Schwengers, Oliver and Jelonek, Lukas and Dieckmann, Marius Alfred and Beyvers, Sebastian and Blom, Jochen and Goesmann, Alexander", 24 </xml>
29 title = "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification", 25 <xml name="citations">
30 journal= "Microbial Genomics", 26 <citations>
31 year = "2021", 27 <citation type="doi">10.1099/mgen.0.000685</citation>
32 volume = "7", 28 </citations>
33 number = "11", 29 </xml>
34 pages = "",
35 doi = "https://doi.org/10.1099/mgen.0.000685",
36 url = "https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000685",
37 publisher = "Microbiology Society",
38 issn = "2057-5858",
39 type = "Journal Article",
40 keywords = "whole-genome sequencing",
41 keywords = "bacteria",
42 keywords = "metagenome-assembled genomes",
43 keywords = "plasmids ",
44 keywords = "genome annotation",
45 eid = "000685",
46 abstract = "Command-line annotation software tools have continuously gained popularity compared to
47 centralized online services due to the worldwide increase of sequenced bacterial genomes.
48 However, results of existing command-line software pipelines heavily depend on taxon-specific
49 databases or sufficiently well annotated reference genomes. Here, we introduce Bakta, a new command-line
50 software tool for the robust, taxon-independent, thorough and, nonetheless, fast annotation of bacterial genomes.
51 Bakta conducts a comprehensive annotation workflow including the detection of small proteins taking into account
52 replicon metadata. The annotation of coding sequences is accelerated via an alignment-free sequence identification
53 approach that in addition facilitates the precise assignment of public database cross-references.
54 Annotation results are exported in GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)-compliant flat files,
55 as well as comprehensive JSON files, facilitating automated downstream analysis.
56 We compared Bakta to other rapid contemporary command-line annotation software tools in both targeted and taxonomically broad benchmarks
57 including isolates and metagenomic-assembled genomes. We demonstrated that Bakta outperforms other tools in terms of functional annotations,
58 the assignment of functional categories and database cross-references, whilst providing comparable wall-clock runtimes.
59 Bakta is implemented in Python 3 and runs on MacOS and Linux systems.
60 It is freely available under a GPLv3 license at https://github.com/oschwengers/bakta.
61 An accompanying web version is available at https://bakta.computational.bio.",
62 }
63 </citation>
64 </citations>
65 </xml>
66 </macros> 30 </macros>