l<tool id="emmtyper" name="emm-typing of S. pyogenes" version="0.1.0+galaxy0">
    <requirements>
        <requirement type="package">emmtyper</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        emmtyper -o '$output1' '$input1'
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta" />
    </inputs>
    <outputs>
        <data name="output1" format="txt" from_work_dir="results.txt" />
    </outputs>
    <help><![CDATA[
        Usage: emmtyper [OPTIONS] [FASTA]...

  Welcome to emmtyper.

  Usage:

  emmtyper *.fasta

Options:
  --version                       Show the version and exit.
  -w, --workflow [blast|pcr]      Choose workflow  [default: blast]
  -d, --blast_db TEXT             Path to EMM BLAST DB
  -k, --keep                      Keep BLAST and isPcr output files.
  -d, --cluster-distance INTEGER  Distance between cluster of matches to
                                  consider as different clusters.  [default:
                                  500]
  -o, --output TEXT               Output stream. Path to file for output to a
                                  file.  [default: stdout]
  -f, --output-format [short|verbose|visual]
                                  Output format.
  --dust [yes|no|level window linker]
                                  [BLAST] Filter query sequence with DUST.
                                  [default: no]
  --percent-identity INTEGER      [BLAST] Minimal percent identity of
                                  sequence.  [default: 95]
  --culling-limit INTEGER         [BLAST] Total hits to return in a position.
                                  [default: 5]
  --mismatch INTEGER              [BLAST] Threshold for number of mismatch to
                                  allow in BLAST hit.  [default: 4]
  --align-diff INTEGER            [BLAST] Threshold for difference between
                                  alignment length and subject length in BLAST
                                  hit.  [default: 5]
  --gap INTEGER                   [BLAST] Threshold gap to allow in BLAST hit.
                                  [default: 2]
  --blast-path TEXT               [BLAST] Specify full path to blastn
                                  executable.
  --primer-db TEXT                [isPcr] PCR primer. Text file with 3
                                  columns: Name, Forward Primer, Reverse
                                  Primer. 
  --min-perfect INTEGER           [isPcr] Minimum size of perfect match at 3'
                                  primer end.  [default: 15]
  --min-good INTEGER              [isPcr] Minimum size where there must be 2
                                  matches for each mismatch.  [default: 15]
  --max-size INTEGER              [isPcr] Maximum size of PCR product.
                                  [default: 2000]
  --ispcr-path TEXT               [isPcr] Specify full path to isPcr
                                  executable.
  --help                          Show this message and exit.

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubemmtyper,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {emmtyper},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/MDU-PHL/emmtyper},
}</citation>
    </citations>
</tool>