|
kkonganti@17
|
1 // Help text for seqkit grep within CPIPES.
|
|
kkonganti@17
|
2
|
|
kkonganti@17
|
3 def seqkitgrepHelp(params) {
|
|
kkonganti@17
|
4
|
|
kkonganti@17
|
5 Map tool = [:]
|
|
kkonganti@17
|
6 Map toolspecs = [:]
|
|
kkonganti@17
|
7 tool.text = [:]
|
|
kkonganti@17
|
8 tool.helpparams = [:]
|
|
kkonganti@17
|
9
|
|
kkonganti@17
|
10 toolspecs = [
|
|
kkonganti@17
|
11 'seqkit_grep_n': [
|
|
kkonganti@17
|
12 clihelp: 'Match by full name instead of just ID. ' +
|
|
kkonganti@17
|
13 "Default: " + (params.seqkit_grep_n ?: 'undefined'),
|
|
kkonganti@17
|
14 cliflag: '--seqkit_grep_n',
|
|
kkonganti@17
|
15 clivalue: (params.seqkit_grep_n ? ' ' : '')
|
|
kkonganti@17
|
16 ],
|
|
kkonganti@17
|
17 'seqkit_grep_s': [
|
|
kkonganti@17
|
18 clihelp: 'Search subseq on seq, both positive and negative ' +
|
|
kkonganti@17
|
19 'strand are searched, and mismatch allowed using flag --seqkit_grep_m. ' +
|
|
kkonganti@17
|
20 "Default: " + (params.seqkit_grep_s ?: 'undefined'),
|
|
kkonganti@17
|
21 cliflag: '--seqkit_grep_s',
|
|
kkonganti@17
|
22 clivalue: (params.seqkit_grep_s ? ' ' : '')
|
|
kkonganti@17
|
23 ],
|
|
kkonganti@17
|
24 'seqkit_grep_c': [
|
|
kkonganti@17
|
25 clihelp: 'Input is circular genome ' +
|
|
kkonganti@17
|
26 "Default: " + (params.seqkit_grep_c ?: 'undefined'),
|
|
kkonganti@17
|
27 cliflag: '--seqkit_grep_c',
|
|
kkonganti@17
|
28 clivalue: (params.seqkit_grep_c ? ' ' : '')
|
|
kkonganti@17
|
29 ],
|
|
kkonganti@17
|
30 'seqkit_grep_C': [
|
|
kkonganti@17
|
31 clihelp: 'Just print a count of matching records. With the ' +
|
|
kkonganti@17
|
32 '--seqkit_grep_v flag, count non-matching records. ' +
|
|
kkonganti@17
|
33 "Default: " + (params.seqkit_grep_v ?: 'undefined'),
|
|
kkonganti@17
|
34 cliflag: '--seqkit_grep_v',
|
|
kkonganti@17
|
35 clivalue: (params.seqkit_grep_v ? ' ' : '')
|
|
kkonganti@17
|
36 ],
|
|
kkonganti@17
|
37 'seqkit_grep_i': [
|
|
kkonganti@17
|
38 clihelp: 'Ignore case while using seqkit grep. ' +
|
|
kkonganti@17
|
39 "Default: " + (params.seqkit_grep_i ?: 'undefined'),
|
|
kkonganti@17
|
40 cliflag: '--seqkit_grep_i',
|
|
kkonganti@17
|
41 clivalue: (params.seqkit_grep_i ? ' ' : '')
|
|
kkonganti@17
|
42 ],
|
|
kkonganti@17
|
43 'seqkit_grep_v': [
|
|
kkonganti@17
|
44 clihelp: 'Invert the match i.e. select non-matching records. ' +
|
|
kkonganti@17
|
45 "Default: " + (params.seqkit_grep_v ?: 'undefined'),
|
|
kkonganti@17
|
46 cliflag: '--seqkit_grep_v',
|
|
kkonganti@17
|
47 clivalue: (params.seqkit_grep_v ? ' ' : '')
|
|
kkonganti@17
|
48 ],
|
|
kkonganti@17
|
49 'seqkit_grep_m': [
|
|
kkonganti@17
|
50 clihelp: 'Maximum mismatches when matching by sequence. ' +
|
|
kkonganti@17
|
51 "Default: " + (params.seqkit_grep_m ?: 'undefined'),
|
|
kkonganti@17
|
52 cliflag: '--seqkit_grep_m',
|
|
kkonganti@17
|
53 clivalue: (params.seqkit_grep_v ?: '')
|
|
kkonganti@17
|
54 ],
|
|
kkonganti@17
|
55 'seqkit_grep_r': [
|
|
kkonganti@17
|
56 clihelp: 'Input patters are regular expressions. ' +
|
|
kkonganti@17
|
57 "Default: " + (params.seqkit_grep_m ?: 'undefined'),
|
|
kkonganti@17
|
58 cliflag: '--seqkit_grep_m',
|
|
kkonganti@17
|
59 clivalue: (params.seqkit_grep_v ?: '')
|
|
kkonganti@17
|
60 ]
|
|
kkonganti@17
|
61 ]
|
|
kkonganti@17
|
62
|
|
kkonganti@17
|
63 toolspecs.each {
|
|
kkonganti@17
|
64 k, v -> tool.text['--' + k] = "${v.clihelp}"
|
|
kkonganti@17
|
65 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
|
|
kkonganti@17
|
66 }
|
|
kkonganti@17
|
67
|
|
kkonganti@17
|
68 return tool
|
|
kkonganti@17
|
69 } |
