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comparison emmtyper.xml @ 0:e72652c6edb9 draft

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author estrain
date Fri, 31 Mar 2023 17:14:38 +0000
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1 l<tool id="emmtyper" name="emm-typing of S. pyogenes" version="0.1.0+galaxy0">
2 <requirements>
3 <requirement type="package">emmtyper</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 emmtyper -o '$output1' '$input1'
7 ]]></command>
8 <inputs>
9 <param type="data" name="input1" format="fasta" />
10 </inputs>
11 <outputs>
12 <data name="output1" format="txt" from_work_dir="results.txt" />
13 </outputs>
14 <help><![CDATA[
15 Usage: emmtyper [OPTIONS] [FASTA]...
16
17 Welcome to emmtyper.
18
19 Usage:
20
21 emmtyper *.fasta
22
23 Options:
24 --version Show the version and exit.
25 -w, --workflow [blast|pcr] Choose workflow [default: blast]
26 -d, --blast_db TEXT Path to EMM BLAST DB
27 -k, --keep Keep BLAST and isPcr output files.
28 -d, --cluster-distance INTEGER Distance between cluster of matches to
29 consider as different clusters. [default:
30 500]
31 -o, --output TEXT Output stream. Path to file for output to a
32 file. [default: stdout]
33 -f, --output-format [short|verbose|visual]
34 Output format.
35 --dust [yes|no|level window linker]
36 [BLAST] Filter query sequence with DUST.
37 [default: no]
38 --percent-identity INTEGER [BLAST] Minimal percent identity of
39 sequence. [default: 95]
40 --culling-limit INTEGER [BLAST] Total hits to return in a position.
41 [default: 5]
42 --mismatch INTEGER [BLAST] Threshold for number of mismatch to
43 allow in BLAST hit. [default: 4]
44 --align-diff INTEGER [BLAST] Threshold for difference between
45 alignment length and subject length in BLAST
46 hit. [default: 5]
47 --gap INTEGER [BLAST] Threshold gap to allow in BLAST hit.
48 [default: 2]
49 --blast-path TEXT [BLAST] Specify full path to blastn
50 executable.
51 --primer-db TEXT [isPcr] PCR primer. Text file with 3
52 columns: Name, Forward Primer, Reverse
53 Primer.
54 --min-perfect INTEGER [isPcr] Minimum size of perfect match at 3'
55 primer end. [default: 15]
56 --min-good INTEGER [isPcr] Minimum size where there must be 2
57 matches for each mismatch. [default: 15]
58 --max-size INTEGER [isPcr] Maximum size of PCR product.
59 [default: 2000]
60 --ispcr-path TEXT [isPcr] Specify full path to isPcr
61 executable.
62 --help Show this message and exit.
63
64 ]]></help>
65 <citations>
66 <citation type="bibtex">
67 @misc{githubemmtyper,
68 author = {LastTODO, FirstTODO},
69 year = {TODO},
70 title = {emmtyper},
71 publisher = {GitHub},
72 journal = {GitHub repository},
73 url = {https://github.com/MDU-PHL/emmtyper},
74 }</citation>
75 </citations>
76 </tool>