Mercurial > repos > estrain > btyper

annotate btyper.xml @ 0:f615242851d6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
author estrain
date Thu, 12 Mar 2026 19:48:47 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
1 <tool id="btyper" name="BTyper" version="3.4">
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
2 <requirements>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
3 <requirement type="package" version="3.4.0">btyper3</requirement>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
4 </requirements>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
6
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
7 btyper3 -i $draft
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
8 -o "./"; cat btyper3_final_results/*.txt > results.txt;
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
9
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
10 ]]></command>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
11 <inputs>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
12 <param name="draft" type="data" format="fasta" label="FASTA" />
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
13 </inputs>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
14 <outputs>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
15 <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
16 </outputs>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
17 <help><![CDATA[
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
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.
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
19
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
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.
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
21
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
22 ]]></help>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
23 <citations>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
24 <citation type="bibtex">
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
25 @misc{carrol_kovac_miller_wiedman_2017,
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
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.},
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
27 url={http://aem.asm.org/content/early/2017/06/12/AEM.01096-17},
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
28 journal={Applied and Environmental Microbiology}, publisher={ASM},
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
29 author={Carroll, Laura M., Jasna Kovac, Rachel A. Miller, Martin Wiedmann},
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
30 year={2017}, month={Jun}} ,
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
31 }</citation>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
32 </citations>
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
33
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
34
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
35
f615242851d6 planemo upload for repository https://github.com/estrain/galaxytrakr-tools/tree/main/tools/btyper commit 1b8023dc06967d4a0eba299c60afc7f09353360b
estrain
parents:
diff changeset
36 </tool>