Mercurial > repos > estrain > btyper
changeset 4:a84469b44fd2 draft
Uploaded
author | estrain |
---|---|
date | Tue, 05 Dec 2017 22:21:59 -0500 |
parents | a4a776850cd1 |
children | 85aa4faba1ef |
files | btyper.xml |
diffstat | 1 files changed, 61 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/btyper.xml Tue Dec 05 22:21:59 2017 -0500 @@ -0,0 +1,61 @@ +<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>