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comparison 0.2.0/lib/help/mlst.nf @ 11:a5f31c44f8c9

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author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 def mlstHelp(params) {
2
3 Map tool = [:]
4 Map toolspecs = [:]
5 tool.text = [:]
6 tool.helpparams = [:]
7
8 toolspecs = [
9 'mlst_run': [
10 clihelp: "Run MLST tool. Default: ${params.mlst_run}",
11 cliflag: null,
12 clivalue: null
13 ],
14 'mlst_legacy': [
15 clihelp: "Use old legacy output with allele header row (requires --mlst_scheme). " +
16 "Default: ${params.mlst_legacy}",
17 cliflag: '--legacy',
18 clivalue: (params.mlst_legacy ? ' ' : '')
19 ],
20 'mlst_scheme': [
21 clihelp: "Don't autodetect, force this scheme on all inputs. " +
22 "Default: ${params.mlst_scheme}",
23 cliflag: '--scheme',
24 clivalue: (params.mlst_scheme ?: null)
25 ],
26 'mlst_minid': [
27 clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " +
28 "Default: ${params.mlst_minid}",
29 cliflag: '--minid',
30 clivalue: (params.mlst_minid ?: 95)
31 ],
32 'mlst_mincov': [
33 clihelp: 'DNA %cov to report partial allele at all [?].' +
34 "Default: ${params.mlst_mincov}",
35 cliflag: '--mincov',
36 clivalue: (params.mlst_mincov ?: 10)
37 ],
38 'mlst_minscore': [
39 clihelp: 'Minumum score out of 100 to match a scheme.' +
40 "Default: ${params.mlst_minscore}",
41 cliflag: '--minscore',
42 clivalue: (params.mlst_minscore ?: 50)
43 ],
44 'mlst_datadir': [
45 clihelp: 'PubMLST data directory. ' +
46 "Default: ${params.mlst_datadir}",
47 cliflag: '--datadir',
48 clivalue: (params.mlst_datadir ?: null)
49 ],
50 'mlst_blastdb': [
51 clihelp: 'BLAST database directory. ' +
52 "Default: ${params.mlst_blastdb}",
53 cliflag: '--blastdb',
54 clivalue: (params.mlst_blastdb ?: null)
55 ]
56 ]
57
58 toolspecs.each {
59 k, v -> tool.text['--' + k] = "${v.clihelp}"
60 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
61 }
62
63 return tool
64 }