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10
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1 <tool id="btyper" name="BTyper" version="3.2.0">
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2 <requirements>
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3 <requirement type="package">btyper3</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6
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7 btyper3 -i $draft
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8 -o "./"; cat btyper3_final_results/*.txt > results.txt;
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10
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9
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10 ]]></command>
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11 <inputs>
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12 <param name="draft" type="data" format="fasta" label="FASTA" />
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13 </inputs>
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14 <outputs>
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15 <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/>
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16 </outputs>
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17 <help><![CDATA[
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18 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.
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19
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20 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.
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21
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22 ]]></help>
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23 <citations>
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24 <citation type="bibtex">
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25 @misc{carrol_kovac_miller_wiedman_2017,
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26 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.},
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27 url={http://aem.asm.org/content/early/2017/06/12/AEM.01096-17},
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28 journal={Applied and Environmental Microbiology}, publisher={ASM},
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29 author={Carroll, Laura M., Jasna Kovac, Rachel A. Miller, Martin Wiedmann},
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30 year={2017}, month={Jun}} ,
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31 }</citation>
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32 </citations>
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33
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34
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35
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36 </tool>
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