Mercurial > repos > estrain > btyper
comparison btyper-2.0.3/btyper.xml @ 0:46ebe89f01ea draft
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author | estrain |
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date | Wed, 06 Dec 2017 06:01:57 -0500 |
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children | 56713cdcff48 |
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1 <tool id="btyper" name="BTyper" version="2.0.3"> | |
2 <requirements> | |
3 <requirement type="package" version="2.7">python</requirement> | |
4 <requirement type="package">biopython</requirement> | |
5 <requirement type="package">blast</requirement> | |
6 </requirements> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 | |
9 $__tool_directory__/btyper | |
10 -t seq | |
11 #if $jobtype.select == "seq" | |
12 -i $jobtype.asm | |
13 #else if $jobtype.select == "draft" | |
14 -i $jobtype.draft --draft_genome | |
15 #end if | |
16 | |
17 -o "./"; cat btyper_final_results/*.txt > results.txt; | |
18 | |
19 ]]></command> | |
20 <inputs> | |
21 <conditional name="jobtype"> | |
22 <param name="select" type="select" label="Assembly or FASTQ Reads?"> | |
23 <option value="draft">Draft Genome</option> | |
24 <option value="seq">Complete Genome</option> | |
25 </param> | |
26 <when value="seq"> | |
27 <param name="asm" type="data" format="fasta" label="FASTA" /> | |
28 </when> | |
29 <when value="draft"> | |
30 <param name="draft" type="data" format="fasta" label="FASTA" /> | |
31 </when> | |
32 </conditional> | |
33 | |
34 </inputs> | |
35 <outputs> | |
36 <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/> | |
37 </outputs> | |
38 <help><![CDATA[ | |
39 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. | |
40 | |
41 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. | |
42 | |
43 ]]></help> | |
44 <citations> | |
45 <citation type="bibtex"> | |
46 @misc{carrol_kovac_miller_wiedman_2017, | |
47 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.}, | |
48 url={http://aem.asm.org/content/early/2017/06/12/AEM.01096-17}, | |
49 journal={Applied and Environmental Microbiology}, publisher={ASM}, | |
50 author={Carroll, Laura M., Jasna Kovac, Rachel A. Miller, Martin Wiedmann}, | |
51 year={2017}, month={Jun}} , | |
52 }</citation> | |
53 </citations> | |
54 | |
55 | |
56 | |
57 </tool> |