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comparison 0.2.0/lib/help/checkm2predict.nf @ 11:a5f31c44f8c9

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author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 // Help text for checkm2 predict within CPIPES.
2
3 def checkm2predictHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'checkm2predict_run': [
12 clihelp: 'Run `checkm2 predict` tool. Default: ' +
13 (params.checkm2predict_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'checkm2predict_quiet': [
18 clihelp: 'Only output errors. ' +
19 "Default: ${params.checkm2predict_quiet}",
20 cliflag: '--quiet',
21 clivalue: (params.checkm2predict_quiet ? ' ' : '')
22 ],
23 'checkm2predict_lowmem': [
24 clihelp: 'Low memory mode. Reduces DIAMOND blocksize to ' +
25 'significantly reduce RAM usage at the expense of longer runtime. ' +
26 "Default: ${params.checkm2predict_lowmem}",
27 cliflag: '--lowmem',
28 clivalue: (params.checkm2predict_lowmem ? ' ' : '')
29 ],
30 'checkm2predict_general': [
31 clihelp: 'Force the use of the general quality prediction model (gradient boost). ' +
32 "Default: ${params.checkm2predict_general}",
33 cliflag: '--general',
34 clivalue: (params.checkm2predict_general ? ' ' : '')
35 ],
36 'checkm2predict_specific': [
37 clihelp: "Force the use of the specific quality prediction model (neural network) " +
38 "Default: ${params.checkm2predict_specific}",
39 cliflag: '--specific',
40 clivalue: (params.checkm2predict_specific ? ' ' : '')
41 ],
42 'checkm2predict_allmodels': [
43 clihelp: 'Output quality prediction for both models for each genome. ' +
44 "Default: ${params.checkm2predict_allmodels}",
45 cliflag: '--allmodels',
46 clivalue: (params.checkm2predict_allmodels ? ' ' : '')
47 ],
48 'checkm2predict_genes': [
49 clihelp: 'Treat input files as protein files. ' +
50 "Default: ${params.checkm2predict_genes}",
51 cliflag: '--genes',
52 clivalue: (params.checkm2predict_genes ? ' ' : '')
53 ],
54 'checkm2predict_x': [
55 clihelp: 'Extension of input files. ' +
56 "Default: ${params.checkm2predict_x}",
57 cliflag: '-x',
58 clivalue: (params.checkm2predict_x ?: '')
59 ],
60 'checkm2predict_tmpdir': [
61 clihelp: 'Specify an alternate directory for temporary files. ' +
62 "Default: ${params.checkm2predict_tmpdir}",
63 cliflag: '--tmpdir',
64 clivalue: (params.checkm2predict_tmpdir ?: '')
65 ],
66 'checkm2predict_rminterfiles': [
67 clihelp: 'Remove all intermediate files (protein files, diamond output). ' +
68 "Default: ${params.checkm2predict_rminterfiles}",
69 cliflag: '--remove_intermediates',
70 clivalue: (params.checkm2predict_rminterfiles ? ' ' : '')
71 ],
72 'checkm2predict_ttable': [
73 clihelp: 'Provide a specific progidal translation table for bins. The default ' +
74 'value of false will automatically determine either 11 or 4. ' +
75 "Default: ${params.checkm2predict_ttable}",
76 cliflag: '--ttable',
77 clivalue: (params.checkm2predict_ttable ? ' ' : '')
78 ],
79 'checkm2predict_dbg_cos': [
80 clihelp: 'DEBUG: Write cosine similarity values to a file. ' +
81 "Default: ${params.checkm2predict_dbg_cos}",
82 cliflag: '--dbg_cos',
83 clivalue: (params.checkm2predict_dbg_cos ? ' ' : '')
84 ],
85 'checkm2predict_dbg_vectors': [
86 clihelp: 'DEBUG: Write Dump pickled feature vectors to a file. ' +
87 "Default: ${params.checkm2predict_dbg_vectors}",
88 cliflag: '--dbg_vectors',
89 clivalue: (params.checkm2predict_dbg_vectors ? ' ' : '')
90 ]
91 ]
92
93 toolspecs.each {
94 k, v -> tool.text['--' + k] = "${v.clihelp}"
95 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
96 }
97
98 return tool
99 }