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