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comparison 1.0.0/lib/help/kmaindex.nf @ 0:0a8dda29956e draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 // Help text for kma index within CPIPES.
2
3 def kmaindexHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'kmaindex_run': [
12 clihelp: 'Run kma index tool. Default: ' +
13 (params.kmaindex_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'kmaindex_t_db': [
18 clihelp: 'Add to existing DB. ' +
19 "Default: ${params.kmaindex_t_db}",
20 cliflag: '-t_db',
21 clivalue: (params.kmaindex_t_db ? ' ' : '')
22 ],
23 'kmaindex_k': [
24 clihelp: 'k-mer size. ' +
25 "Default: ${params.kmaindex_k}",
26 cliflag: '-k',
27 clivalue: (params.kmaindex_k ?: '')
28 ],
29 'kmaindex_m': [
30 clihelp: 'Minimizer size. ' +
31 "Default: ${params.kmaindex_m}",
32 cliflag: '-m',
33 clivalue: (params.kmaindex_m ?: '')
34 ],
35 'kmaindex_hc': [
36 clihelp: 'Homopolymer compression. ' +
37 "Default: ${params.kmaindex_hc}",
38 cliflag: '-hc',
39 clivalue: (params.kmaindex_hc ? ' ' : '')
40 ],
41 'kmaindex_ML': [
42 clihelp: 'Minimum length of templates. Defaults to --kmaindex_k ' +
43 "Default: ${params.kmaindex_ML}",
44 cliflag: '-ML',
45 clivalue: (params.kmaindex_ML ?: '')
46 ],
47 'kmaindex_ME': [
48 clihelp: 'Mega DB. ' +
49 "Default: ${params.kmaindex_ME}",
50 cliflag: '-ME',
51 clivalue: (params.kmaindex_ME ? ' ' : '')
52 ],
53 'kmaindex_Sparse': [
54 clihelp: 'Make Sparse DB. ' +
55 "Default: ${params.kmaindex_Sparse}",
56 cliflag: '-Sparse',
57 clivalue: (params.kmaindex_Sparse ? ' ' : '')
58 ],
59 'kmaindex_ht': [
60 clihelp: 'Homology template. ' +
61 "Default: ${params.kmaindex_ht}",
62 cliflag: '-ht',
63 clivalue: (params.kmaindex_ht ?: '')
64 ],
65 'kmaindex_hq': [
66 clihelp: 'Homology query. ' +
67 "Default: ${params.kmaindex_hq}",
68 cliflag: '-hq',
69 clivalue: (params.kmaindex_hq ?: '')
70 ],
71 'kmaindex_and': [
72 clihelp: 'Both homology thresholds have to reach. ' +
73 "Default: ${params.kmaindex_and}",
74 cliflag: '-and',
75 clivalue: (params.kmaindex_and ? ' ' : '')
76 ],
77 'kmaindex_nbp': [
78 clihelp: 'No bias print. ' +
79 "Default: ${params.kmaindex_nbp}",
80 cliflag: '-nbp',
81 clivalue: (params.kmaindex_nbp ? ' ' : '')
82 ]
83 ]
84
85 toolspecs.each {
86 k, v -> tool.text['--' + k] = "${v.clihelp}"
87 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
88 }
89
90 return tool
91 }