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1 <tool id="btyper" name="BTyper" version="2.0.3">
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2 <requirements>
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3 <requirement type="package" version="2.7">python</requirement>
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4 <requirement type="package">biopython</requirement>
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5 <requirement type="package">blast</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8
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9
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9 python $__tool_directory__/btyper
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10 -t seq
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11 #if $jobtype.select == "seq"
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12 -i $jobtype.asm
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13 #else if $jobtype.select == "draft"
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14 -i $jobtype.draft --draft_genome
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15 #end if
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16
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17 -o "./"; cat btyper_final_results/*.txt > results.txt;
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18
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19 ]]></command>
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20 <inputs>
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21 <conditional name="jobtype">
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22 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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23 <option value="draft">Draft Genome</option>
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24 <option value="seq">Complete Genome</option>
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25 </param>
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26 <when value="seq">
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27 <param name="asm" type="data" format="fasta" label="FASTA" />
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28 </when>
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29 <when value="draft">
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30 <param name="draft" type="data" format="fasta" label="FASTA" />
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31 </when>
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32 </conditional>
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33
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34 </inputs>
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35 <outputs>
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36 <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/>
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37 </outputs>
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38 <help><![CDATA[
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39 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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40
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41 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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42
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43 ]]></help>
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44 <citations>
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45 <citation type="bibtex">
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46 @misc{carrol_kovac_miller_wiedman_2017,
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47 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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48 url={http://aem.asm.org/content/early/2017/06/12/AEM.01096-17},
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49 journal={Applied and Environmental Microbiology}, publisher={ASM},
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50 author={Carroll, Laura M., Jasna Kovac, Rachel A. Miller, Martin Wiedmann},
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51 year={2017}, month={Jun}} ,
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52 }</citation>
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53 </citations>
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54
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55
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56
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57 </tool>
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