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comparison 0.5.0/lib/help/seqkitgrep.nf @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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-1:000000000000 0:97cd2f532efe
1 // Help text for seqkit `grep` within CPIPES.
2
3 def seqkitgrepHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'seqkit_grep_run': [
12 clihelp: 'Run the seqkit `grep` tool. Default: ' +
13 (params.seqkit_grep_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'seqkit_grep_n': [
18 clihelp: 'Match by full name instead of just ID. ' +
19 "Default: " + (params.seqkit_grep_n ?: 'undefined'),
20 cliflag: '--seqkit_grep_n',
21 clivalue: (params.seqkit_grep_n ? ' ' : '')
22 ],
23 'seqkit_grep_s': [
24 clihelp: 'Search subseq on seq, both positive and negative ' +
25 'strand are searched, and mismatch allowed using flag --seqkit_grep_m. ' +
26 "Default: " + (params.seqkit_grep_s ?: 'undefined'),
27 cliflag: '--seqkit_grep_s',
28 clivalue: (params.seqkit_grep_s ? ' ' : '')
29 ],
30 'seqkit_grep_c': [
31 clihelp: 'Input is circular genome ' +
32 "Default: " + (params.seqkit_grep_c ?: 'undefined'),
33 cliflag: '--seqkit_grep_c',
34 clivalue: (params.seqkit_grep_c ? ' ' : '')
35 ],
36 'seqkit_grep_C': [
37 clihelp: 'Just print a count of matching records. With the ' +
38 '--seqkit_grep_v flag, count non-matching records. ' +
39 "Default: " + (params.seqkit_grep_v ?: 'undefined'),
40 cliflag: '--seqkit_grep_v',
41 clivalue: (params.seqkit_grep_v ? ' ' : '')
42 ],
43 'seqkit_grep_i': [
44 clihelp: 'Ignore case while using seqkit grep. ' +
45 "Default: " + (params.seqkit_grep_i ?: 'undefined'),
46 cliflag: '--seqkit_grep_i',
47 clivalue: (params.seqkit_grep_i ? ' ' : '')
48 ],
49 'seqkit_grep_v': [
50 clihelp: 'Invert the match i.e. select non-matching records. ' +
51 "Default: " + (params.seqkit_grep_v ?: 'undefined'),
52 cliflag: '--seqkit_grep_v',
53 clivalue: (params.seqkit_grep_v ? ' ' : '')
54 ],
55 'seqkit_grep_m': [
56 clihelp: 'Maximum mismatches when matching by sequence. ' +
57 "Default: " + (params.seqkit_grep_m ?: 'undefined'),
58 cliflag: '--seqkit_grep_m',
59 clivalue: (params.seqkit_grep_v ?: '')
60 ],
61 'seqkit_grep_r': [
62 clihelp: 'Input patters are regular expressions. ' +
63 "Default: " + (params.seqkit_grep_m ?: 'undefined'),
64 cliflag: '--seqkit_grep_m',
65 clivalue: (params.seqkit_grep_v ?: '')
66 ]
67 ]
68
69 toolspecs.each {
70 k, v -> tool.text['--' + k] = "${v.clihelp}"
71 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
72 }
73
74 return tool
75 }