Mercurial > repos > estrain > btyper
changeset 17:18fa9b4a6309 draft
Deleted selected files
author | estrain |
---|---|
date | Wed, 06 Dec 2017 05:50:10 -0500 |
parents | 1eb237c630cb |
children | c0eb3a156508 |
files | btyper-2.0.3/btyper.xml |
diffstat | 1 files changed, 0 insertions(+), 57 deletions(-) [+] |
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--- a/btyper-2.0.3/btyper.xml Wed Dec 06 05:47:40 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -<tool id="btyper" name="BTyper" version="2.0.3"> - <requirements> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package">biopython</requirement> - <requirement type="package">blast</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - - $__tool_directory__/btyper - -t seq - #if $jobtype.select == "seq" - -i $jobtype.asm - #else if $jobtype.select == "draft" - -i $jobtype.draft --draft_genome - #end if - - -o "./"; cat btyper_final_results/*.txt > results.txt; - - ]]></command> - <inputs> - <conditional name="jobtype"> - <param name="select" type="select" label="Assembly or FASTQ Reads?"> - <option value="draft">Draft Genome</option> - <option value="seq">Complete Genome</option> - </param> - <when value="seq"> - <param name="asm" type="data" format="fasta" label="FASTA" /> - </when> - <when value="draft"> - <param name="draft" type="data" format="fasta" label="FASTA" /> - </when> - </conditional> - - </inputs> - <outputs> - <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/> - </outputs> - <help><![CDATA[ - TODO: Fill in help. - ]]></help> - 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. - - 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. - <citations> - <citation type="bibtex"> - @misc{carrol_kovac_miller_wiedman_2017, - 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.}, - url={http://aem.asm.org/content/early/2017/06/12/AEM.01096-17}, - journal={Applied and Environmental Microbiology}, publisher={ASM}, - author={Carroll, Laura M., Jasna Kovac, Rachel A. Miller, Martin Wiedmann}, - year={2017}, month={Jun}} , - }</citation> - </citations> - - - -</tool>