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comparison 0.7.0/lib/help/sourmashsigkmers.nf @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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16:b90e5a7a3d4f 17:0e7a0053e4a6
1 // Help text for sourmash sigkmers within CPIPES.
2
3 def sourmashsigkmersHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'sourmashsigkmers_run': [
12 clihelp: 'Run `sourmash sigkmers` tool. Default: ' +
13 (params.sourmashsigkmers_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'sourmashsigkmers_k': [
18 clihelp: 'The k-mer size to select. ' +
19 "Default: ${params.sourmashsigkmers_k}",
20 cliflag: '-k',
21 clivalue: (params.sourmashsigkmers_k ?: '')
22 ],
23 'sourmashsigkmers_protein': [
24 clihelp: 'Choose a protein signature. ' +
25 "Default: ${params.sourmashsigkmers_protein}",
26 cliflag: '--protein',
27 clivalue: (params.sourmashsigkmers_protein ? ' ' : '')
28 ],
29 'sourmashsigkmers_noprotein': [
30 clihelp: 'Do not choose a protein signature. ' +
31 "Default: ${params.sourmashsigkmers_noprotein}",
32 cliflag: '--no-protein',
33 clivalue: (params.sourmashsigkmers_noprotein ? ' ' : '')
34 ],
35 'sourmashsigkmers_dayhoff': [
36 clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
37 "Default: ${params.sourmashsigkmers_dayhoff}",
38 cliflag: '--dayhoff',
39 clivalue: (params.sourmashsigkmers_dayhoff ? ' ' : '')
40 ],
41 'sourmashsigkmers_nodayhoff': [
42 clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
43 "Default: ${params.sourmashsigkmers_nodayhoff}",
44 cliflag: '--no-dayhoff',
45 clivalue: (params.sourmashsigkmers_nodayhoff ? ' ' : '')
46 ],
47 'sourmashsigkmers_hp': [
48 clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
49 "Default: ${params.sourmashsigkmers_hp}",
50 cliflag: '--hp',
51 clivalue: (params.sourmashsigkmers_hp ? ' ' : '')
52 ],
53 'sourmashsigkmers_nohp': [
54 clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
55 "Default: ${params.sourmashsigkmers_nohp}",
56 cliflag: '--no-hp',
57 clivalue: (params.sourmashsigkmers_nohp ? ' ' : '')
58 ],
59 'sourmashsigkmers_dna': [
60 clihelp: 'Choose DNA signature. ' +
61 "Default: ${params.sourmashsigkmers_dna}",
62 cliflag: '--dna',
63 clivalue: (params.sourmashsigkmers_dna ? ' ' : '')
64 ],
65 'sourmashsigkmers_nodna': [
66 clihelp: 'Do not choose DNA signature. ' +
67 "Default: ${params.sourmashsigkmers_nodna}",
68 cliflag: '--no-dna',
69 clivalue: (params.sourmashsigkmers_nodna ? ' ' : '')
70 ],
71 'sourmashsigkmers_save_kmers': [
72 clihelp: 'Save k-mers and hash values to a CSV file. ' +
73 "Default: ${params.sourmashsigkmers_save_kmers}",
74 cliflag: null,
75 clivalue: null
76 ],
77 'sourmashsigkmers_save_seqs': [
78 clihelp: 'Save sequences with matching hash values to a FASTA file. ' +
79 "Default: ${params.sourmashsigkmers_save_seqs}",
80 cliflag: null,
81 clivalue: null
82 ],
83 'sourmashsigkmers_translate': [
84 clihelp: 'Translate DNA k-mers into amino acids (for protein, dayhoff, and hp sketches). ' +
85 "Default: ${params.sourmashsigkmers_translate}",
86 cliflag: '--translate',
87 clivalue: (params.sourmashsigkmers_translate ? ' ' : '')
88 ]
89 ]
90
91 toolspecs.each {
92 k, v -> tool.text['--' + k] = "${v.clihelp}"
93 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
94 }
95
96 return tool
97 }