<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[

      $__tool_directory__/btyper
      -t seq     
      #if $jobtype.select == "seq"
        -i $jobtype.asm  
      #else if $jobtype.select == "draft"
        -i $jobtype.draft --draft_genome
      #end if

      -o "./"; cat btyper_final_results/*.txt > results.txt; 

    ]]></command>
    <inputs>
      <conditional name="jobtype">
        <param name="select" type="select" label="Assembly or FASTQ Reads?">
          <option value="draft">Draft Genome</option>
          <option value="seq">Complete Genome</option>
        </param>
        <when value="seq">
          <param name="asm" type="data" format="fasta" label="FASTA" />
        </when>
        <when value="draft">
          <param name="draft" type="data" format="fasta" label="FASTA" />
        </when>
      </conditional>

    </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>