estrain@1: l<tool id="emmtyper" name="emm-typing of S. pyogenes" version="0.1.0+galaxy0" python_template_version="3.5">
estrain@0:     <requirements>
estrain@0:         <requirement type="package">emmtyper</requirement>
estrain@0:     </requirements>
estrain@0:     <command detect_errors="exit_code"><![CDATA[
estrain@0:         emmtyper -o '$output1' '$input1'
estrain@0:     ]]></command>
estrain@0:     <inputs>
estrain@0:         <param type="data" name="input1" format="fasta" />
estrain@0:     </inputs>
estrain@0:     <outputs>
estrain@0:         <data name="output1" format="txt" from_work_dir="results.txt" />
estrain@0:     </outputs>
estrain@0:     <help><![CDATA[
estrain@0:         Usage: emmtyper [OPTIONS] [FASTA]...
estrain@0: 
estrain@0:   Welcome to emmtyper.
estrain@0: 
estrain@0:   Usage:
estrain@0: 
estrain@0:   emmtyper *.fasta
estrain@0: 
estrain@0: Options:
estrain@0:   --version                       Show the version and exit.
estrain@0:   -w, --workflow [blast|pcr]      Choose workflow  [default: blast]
estrain@0:   -d, --blast_db TEXT             Path to EMM BLAST DB
estrain@0:   -k, --keep                      Keep BLAST and isPcr output files.
estrain@0:   -d, --cluster-distance INTEGER  Distance between cluster of matches to
estrain@0:                                   consider as different clusters.  [default:
estrain@0:                                   500]
estrain@0:   -o, --output TEXT               Output stream. Path to file for output to a
estrain@0:                                   file.  [default: stdout]
estrain@0:   -f, --output-format [short|verbose|visual]
estrain@0:                                   Output format.
estrain@0:   --dust [yes|no|level window linker]
estrain@0:                                   [BLAST] Filter query sequence with DUST.
estrain@0:                                   [default: no]
estrain@0:   --percent-identity INTEGER      [BLAST] Minimal percent identity of
estrain@0:                                   sequence.  [default: 95]
estrain@0:   --culling-limit INTEGER         [BLAST] Total hits to return in a position.
estrain@0:                                   [default: 5]
estrain@0:   --mismatch INTEGER              [BLAST] Threshold for number of mismatch to
estrain@0:                                   allow in BLAST hit.  [default: 4]
estrain@0:   --align-diff INTEGER            [BLAST] Threshold for difference between
estrain@0:                                   alignment length and subject length in BLAST
estrain@0:                                   hit.  [default: 5]
estrain@0:   --gap INTEGER                   [BLAST] Threshold gap to allow in BLAST hit.
estrain@0:                                   [default: 2]
estrain@0:   --blast-path TEXT               [BLAST] Specify full path to blastn
estrain@0:                                   executable.
estrain@0:   --primer-db TEXT                [isPcr] PCR primer. Text file with 3
estrain@0:                                   columns: Name, Forward Primer, Reverse
estrain@0:                                   Primer. 
estrain@0:   --min-perfect INTEGER           [isPcr] Minimum size of perfect match at 3'
estrain@0:                                   primer end.  [default: 15]
estrain@0:   --min-good INTEGER              [isPcr] Minimum size where there must be 2
estrain@0:                                   matches for each mismatch.  [default: 15]
estrain@0:   --max-size INTEGER              [isPcr] Maximum size of PCR product.
estrain@0:                                   [default: 2000]
estrain@0:   --ispcr-path TEXT               [isPcr] Specify full path to isPcr
estrain@0:                                   executable.
estrain@0:   --help                          Show this message and exit.
estrain@0: 
estrain@0:     ]]></help>
estrain@0:     <citations>
estrain@0:         <citation type="bibtex">
estrain@0: @misc{githubemmtyper,
estrain@0:   author = {LastTODO, FirstTODO},
estrain@0:   year = {TODO},
estrain@0:   title = {emmtyper},
estrain@0:   publisher = {GitHub},
estrain@0:   journal = {GitHub repository},
estrain@0:   url = {https://github.com/MDU-PHL/emmtyper},
estrain@0: }</citation>
estrain@0:     </citations>
estrain@0: </tool>