Mercurial > repos > estrain > btyper
comparison btyper-3.2.0/btyper.xml @ 10:7681f3c28536 draft
Uploaded
author | estrain |
---|---|
date | Tue, 17 May 2022 02:04:14 +0000 |
parents | |
children | d4af9796b682 |
comparison
equal
deleted
inserted
replaced
9:56713cdcff48 | 10:7681f3c28536 |
---|---|
1 <tool id="btyper" name="BTyper" version="3.2.0"> | |
2 <requirements> | |
3 <requirement type="package">btyper3</requirement> | |
4 </requirements> | |
5 <command detect_errors="exit_code"><![CDATA[ | |
6 | |
7 btyper3 -i $draft | |
8 -o "./"; cat btyper_final_results/*.txt > results.txt; | |
9 | |
10 ]]></command> | |
11 <inputs> | |
12 <param name="draft" type="data" format="fasta" label="FASTA" /> | |
13 </inputs> | |
14 <outputs> | |
15 <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/> | |
16 </outputs> | |
17 <help><![CDATA[ | |
18 BTyper is a that employs a combination of (i) virulence gene-based typing, (ii) multi-locus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B. cereus group isolates using nucleotide sequencing data. | |
19 | |
20 The Draft Genome option concatenates contigs in a single fasta file and produces a single report. The Complete Genome option assumes a single chromosome, and plasmids if present, and the report contains a section for each fasta header in the input file. | |
21 | |
22 ]]></help> | |
23 <citations> | |
24 <citation type="bibtex"> | |
25 @misc{carrol_kovac_miller_wiedman_2017, | |
26 title={Rapid, high-throughput identification of anthrax-causing and emetic Bacillus cereus group genome assemblies using BTyper, a computational tool for virulence-based classification of Bacillus cereus group isolates using nucleotide sequencing data.}, | |
27 url={http://aem.asm.org/content/early/2017/06/12/AEM.01096-17}, | |
28 journal={Applied and Environmental Microbiology}, publisher={ASM}, | |
29 author={Carroll, Laura M., Jasna Kovac, Rachel A. Miller, Martin Wiedmann}, | |
30 year={2017}, month={Jun}} , | |
31 }</citation> | |
32 </citations> | |
33 | |
34 | |
35 | |
36 </tool> |