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1 l<tool id="emmtyper" name="emm-typing of S. pyogenes" version="0.1.0+galaxy0">
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2 <requirements>
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3 <requirement type="package">emmtyper</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 emmtyper -o '$output1' '$input1'
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7 ]]></command>
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8 <inputs>
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9 <param type="data" name="input1" format="fasta" />
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10 </inputs>
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11 <outputs>
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12 <data name="output1" format="txt" from_work_dir="results.txt" />
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13 </outputs>
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14 <help><![CDATA[
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15 Usage: emmtyper [OPTIONS] [FASTA]...
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16
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17 Welcome to emmtyper.
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18
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19 Usage:
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20
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21 emmtyper *.fasta
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22
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23 Options:
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24 --version Show the version and exit.
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25 -w, --workflow [blast|pcr] Choose workflow [default: blast]
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26 -d, --blast_db TEXT Path to EMM BLAST DB
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27 -k, --keep Keep BLAST and isPcr output files.
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28 -d, --cluster-distance INTEGER Distance between cluster of matches to
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29 consider as different clusters. [default:
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30 500]
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31 -o, --output TEXT Output stream. Path to file for output to a
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32 file. [default: stdout]
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33 -f, --output-format [short|verbose|visual]
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34 Output format.
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35 --dust [yes|no|level window linker]
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36 [BLAST] Filter query sequence with DUST.
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37 [default: no]
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38 --percent-identity INTEGER [BLAST] Minimal percent identity of
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39 sequence. [default: 95]
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40 --culling-limit INTEGER [BLAST] Total hits to return in a position.
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41 [default: 5]
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42 --mismatch INTEGER [BLAST] Threshold for number of mismatch to
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43 allow in BLAST hit. [default: 4]
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44 --align-diff INTEGER [BLAST] Threshold for difference between
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45 alignment length and subject length in BLAST
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46 hit. [default: 5]
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47 --gap INTEGER [BLAST] Threshold gap to allow in BLAST hit.
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48 [default: 2]
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49 --blast-path TEXT [BLAST] Specify full path to blastn
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50 executable.
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51 --primer-db TEXT [isPcr] PCR primer. Text file with 3
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52 columns: Name, Forward Primer, Reverse
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53 Primer.
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54 --min-perfect INTEGER [isPcr] Minimum size of perfect match at 3'
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55 primer end. [default: 15]
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56 --min-good INTEGER [isPcr] Minimum size where there must be 2
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57 matches for each mismatch. [default: 15]
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58 --max-size INTEGER [isPcr] Maximum size of PCR product.
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59 [default: 2000]
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60 --ispcr-path TEXT [isPcr] Specify full path to isPcr
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61 executable.
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62 --help Show this message and exit.
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63
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64 ]]></help>
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65 <citations>
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66 <citation type="bibtex">
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67 @misc{githubemmtyper,
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68 author = {LastTODO, FirstTODO},
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69 year = {TODO},
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70 title = {emmtyper},
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71 publisher = {GitHub},
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72 journal = {GitHub repository},
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73 url = {https://github.com/MDU-PHL/emmtyper},
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74 }</citation>
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75 </citations>
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76 </tool>
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