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

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author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 // Help text for prodigal within CPIPES.
2
3 def prodigalHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'prodigal_run': [
12 clihelp: 'Run prodigal tool. Default: ' +
13 (params.prodigal_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'prodigal_c': [
18 clihelp: 'Closed ends. Do not allow genes to run off edges. ' +
19 "Default: ${params.prodigal_c}",
20 cliflag: '--c',
21 clivalue: (params.prodigal_c ? ' ' : '')
22 ],
23 'prodigal_f': [
24 clihelp: "Select output format (gbk, gff, or sco). " +
25 "Default: ${params.prodigal_f}",
26 cliflag: '-f',
27 clivalue: (params.prodigal_f ?: '')
28 ],
29 'prodigal_g': [
30 clihelp: "Specify translation table to use." +
31 "Default: ${params.prodigal_g}",
32 cliflag: '-g',
33 clivalue: (params.prodigal_g ?: '')
34 ],
35 'prodigal_m': [
36 clihelp: "Treat runs of N as masked sequence; don't build genes " +
37 'across them. ' +
38 "Default: ${params.prodigal_m}",
39 cliflag: '-m',
40 clivalue: (params.prodigal_m ? ' ' : '')
41 ],
42 'prodigal_n': [
43 clihelp: 'Bypass Shine-Dalgarno trainer and force a full motif scan. ' +
44 "Default: ${params.prodigal_n}",
45 cliflag: '-n',
46 clivalue: (params.prodigal_n ? ' ' : '')
47 ],
48 'prodigal_p': [
49 clihelp: "Select procedure (single or meta). " +
50 "Default: ${params.prodigal_p}",
51 cliflag: '-p',
52 clivalue: (params.prodigal_p ?: '')
53 ],
54 'prodigal_t': [
55 clihelp: 'Write a training file (if none exists) ending in suffix `.trnd`; ' +
56 'otherwise, read and use the specified training file. ' +
57 "Default: ${params.prodigal_t}",
58 cliflag: '-t',
59 clivalue: (params.prodigal_t ? ' ' : '')
60 ]
61 ]
62
63 toolspecs.each {
64 k, v -> tool.text['--' + k] = "${v.clihelp}"
65 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
66 }
67
68 return tool
69 }