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comparison 0.2.0/lib/help/kmaindex.nf @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
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 <<<<<<< HEAD
20 "Defaut: ${params.kmaindex_t_db}",
21 =======
22 "Default: ${params.kmaindex_t_db}",
23 >>>>>>> 0.5.0
24 cliflag: '-t_db',
25 clivalue: (params.kmaindex_t_db ? ' ' : '')
26 ],
27 'kmaindex_k': [
28 clihelp: 'k-mer size. ' +
29 "Default: ${params.kmaindex_k}",
30 cliflag: '-k',
31 clivalue: (params.kmaindex_k ?: '')
32 ],
33 'kmaindex_m': [
34 clihelp: 'Minimizer size. ' +
35 "Default: ${params.kmaindex_m}",
36 cliflag: '-m',
37 clivalue: (params.kmaindex_m ?: '')
38 ],
39 'kmaindex_hc': [
40 clihelp: 'Homopolymer compression. ' +
41 "Default: ${params.kmaindex_hc}",
42 cliflag: '-hc',
43 clivalue: (params.kmaindex_hc ? ' ' : '')
44 ],
45 'kmaindex_ML': [
46 clihelp: 'Minimum length of templates. Defaults to --kmaindex_k ' +
47 "Default: ${params.kmaindex_ML}",
48 cliflag: '-ML',
49 clivalue: (params.kmaindex_ML ?: '')
50 ],
51 'kmaindex_ME': [
52 clihelp: 'Mega DB. ' +
53 "Default: ${params.kmaindex_ME}",
54 cliflag: '-ME',
55 clivalue: (params.kmaindex_ME ? ' ' : '')
56 ],
57 'kmaindex_Sparse': [
58 clihelp: 'Make Sparse DB. ' +
59 "Default: ${params.kmaindex_Sparse}",
60 cliflag: '-Sparse',
61 clivalue: (params.kmaindex_Sparse ? ' ' : '')
62 ],
63 'kmaindex_ht': [
64 clihelp: 'Homology template. ' +
65 "Default: ${params.kmaindex_ht}",
66 cliflag: '-ht',
67 clivalue: (params.kmaindex_ht ?: '')
68 ],
69 'kmaindex_hq': [
70 clihelp: 'Homology query. ' +
71 "Default: ${params.kmaindex_hq}",
72 cliflag: '-hq',
73 clivalue: (params.kmaindex_hq ?: '')
74 ],
75 'kmaindex_and': [
76 clihelp: 'Both homology thresholds have to reach. ' +
77 "Default: ${params.kmaindex_and}",
78 cliflag: '-and',
79 clivalue: (params.kmaindex_and ? ' ' : '')
80 ],
81 'kmaindex_nbp': [
82 clihelp: 'No bias print. ' +
83 "Default: ${params.kmaindex_nbp}",
84 cliflag: '-nbp',
85 clivalue: (params.kmaindex_nbp ? ' ' : '')
86 ]
87 ]
88
89 toolspecs.each {
90 k, v -> tool.text['--' + k] = "${v.clihelp}"
91 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
92 }
93
94 return tool
95 }