Mercurial > repos > estrain > btyper
changeset 14:90984da4b414 draft default tip
Uploaded
| author | estrain |
|---|---|
| date | Wed, 13 Nov 2024 20:46:19 +0000 |
| parents | f3afcc9477c0 |
| children | |
| files | btyper/._btyper.xml btyper/btyper.xml btyper/btyper/._btyper.xml btyper/btyper/btyper.xml |
| diffstat | 4 files changed, 36 insertions(+), 36 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/btyper/btyper.xml Wed Nov 13 20:46:19 2024 +0000 @@ -0,0 +1,36 @@ +<tool id="btyper" name="BTyper" version="3.4.0"> + <requirements> + <requirement type="package">btyper3</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + btyper3 -i $draft + -o "./"; cat btyper3_final_results/*.txt > results.txt; + + ]]></command> + <inputs> + <param name="draft" type="data" format="fasta" label="FASTA" /> + </inputs> + <outputs> + <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/> + </outputs> + <help><![CDATA[ + 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. + + ]]></help> + <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>
--- a/btyper/btyper/btyper.xml Wed Nov 13 20:43:49 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -<tool id="btyper" name="BTyper" version="3.4.0"> - <requirements> - <requirement type="package">btyper3</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - - btyper3 -i $draft - -o "./"; cat btyper3_final_results/*.txt > results.txt; - - ]]></command> - <inputs> - <param name="draft" type="data" format="fasta" label="FASTA" /> - </inputs> - <outputs> - <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/> - </outputs> - <help><![CDATA[ - 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. - - ]]></help> - <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>