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comparison 0.7.0/lib/help/tuspy.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 get_top_unique_mash_hit_genomes.py (tuspy) within CPIPES.
2
3 def tuspyHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'tuspy_run': [
12 clihelp: 'Run the get_top_unique_mash_hits_genomes.py ' +
13 'script. Default: ' +
14 (params.tuspy_run ?: false),
15 cliflag: null,
16 clivalue: null
17 ],
18 'tuspy_s': [
19 clihelp: 'Absolute UNIX path to metadata text file with the ' +
20 'field separator, | and ' +
21 '5 fields: serotype|asm_lvl|asm_url|snp_cluster_id' +
22 'Ex: serotype=Derby,antigen_formula=4:f,g:-|Scaffold|402440|ftp://...' +
23 '|PDS000096654.2. Mentioning this option will create a pickle file for the ' +
24 'provided metadata and exits.' +
25 " Default: ${params.tuspy_s}",
26 cliflag: '-s',
27 clivalue: (params.tuspy_s ?: '')
28 ],
29 'tuspy_m': [
30 clihelp: 'Absolute UNIX path to mash screen results file.' +
31 " Default: ${params.tuspy_m}",
32 cliflag: '-m',
33 clivalue: (params.tuspy_m ?: '')
34 ],
35 'tuspy_ps': [
36 clihelp: 'Absolute UNIX Path to serialized metadata object ' +
37 'in a pickle file.' +
38 " Default: ${params.tuspy_ps}",
39 cliflag: '-ps',
40 clivalue: (params.tuspy_ps ?: '')
41 ],
42 'tuspy_gd': [
43 clihelp: 'Absolute UNIX Path to directory containing ' +
44 'gzipped genome FASTA files.' +
45 " Default: ${params.tuspy_gd}",
46 cliflag: '-gd',
47 clivalue: (params.tuspy_gd ?: '')
48 ],
49 'tuspy_gds': [
50 clihelp: 'Genome FASTA file suffix to search for in the ' +
51 'genome directory.' +
52 " Default: ${params.tuspy_gds}",
53 cliflag: '-gds',
54 clivalue: (params.tuspy_gds ?: '')
55 ],
56 'tuspy_n': [
57 clihelp: 'Return up to this many number of top N unique ' +
58 'genome accession hits.' +
59 " Default: ${params.tuspy_n}",
60 cliflag: '-n',
61 clivalue: (params.tuspy_n ?: '')
62 ],
63 'tuspy_skip': [
64 clihelp: 'Skip all hits which belong to the following bioproject ' +
65 'accession(s). A comma separated list of more than one bioproject. ' +
66 " Default: ${params.tuspy_skip}",
67 cliflag: '-skip',
68 clivalue: (params.tuspy_skip ?: '')
69 ]
70 ]
71
72 toolspecs.each {
73 k, v -> tool.text['--' + k] = "${v.clihelp}"
74 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
75 }
76
77 return tool
78 }