Mercurial > repos > estrain > btyper
changeset 3:a4a776850cd1 draft
Deleted selected files
| author | estrain |
|---|---|
| date | Tue, 05 Dec 2017 22:21:39 -0500 |
| parents | d0609c749f37 |
| children | a84469b44fd2 |
| files | btyper.xml |
| diffstat | 1 files changed, 0 insertions(+), 61 deletions(-) [+] |
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--- a/btyper.xml Tue Dec 05 22:21:34 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +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[ - btyper - -t $jobtype.select - #if $jobtype.select == "seq" - -i $jobtype.asm - #esle if $jobtype.select == "se" - -i $jobtype.fastq1 - #esle if $jobtype.select == "pe" - -i $jobtype.fastq1 $jobtype.fastq2 - #end if - - -o "./" - - ]]></command> - <inputs> - <conditional name="jobtype"> - <param name="select" type="select" label="Assembly or FASTQ Reads?"> - <option value="seq">Assembly (fasta)</option> - <option value="se">Single-end FASTQ</option> - <option value="pe">Paired-end FASTQ</option> - </param> - <when value="seq"> - <param name="asm" type="data" format="fasta" label="FASTA" /> - </when> - <when value="se"> - <param name="fastq1" type="data" format="fastq" label="FASTQ file" help="FASTQ" /> - </when> - <when value="pe"> - <param name="fastq1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ" /> - <param name="fastq2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ" /> - </when> - </conditional> - - </inputs> - <outputs> - <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/> - </outputs> - <help><![CDATA[ - TODO: Fill in help. - ]]></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>