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comparison 0.2.0/lib/help/dpubmlstpy.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 dl_pubmlst_profiles_and_schemes.py (dpubmlstpy) within CPIPES.
2
3 def dpubmlstpyHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'dpubmlstpy_run': [
12 clihelp: 'Run the dl_pubmlst_profiles_and_schemes.py ' +
13 'script. Default: ' +
14 (params.dpubmlstpy_run ?: false),
15 cliflag: null,
16 clivalue: null
17 ],
18 'dpubmlstpy_org': [
19 clihelp: 'The organism name to download the MLST alleles ' +
20 'FASTA and profile CSV for. ' +
21 " Default: ${params.dpubmlstpy_org}",
22 cliflag: '-org',
23 clivalue: (params.dpubmlstpy_org ?: '')
24 ],
25 'dpubmlstpy_mlsts': [
26 clihelp: 'The MLST scheme ID to download. ' +
27 " Default: ${params.dpubmlstpy_mlsts}",
28 cliflag: '-mlsts',
29 clivalue: (params.dpubmlstpy_mlsts ?: '')
30 ],
31 'dpubmlstpy_profile': [
32 clihelp: 'The MLST profile name in the scheme. ' +
33 " Default: ${params.dpubmlstpy_profile}",
34 cliflag: '-profile',
35 clivalue: (params.dpubmlstpy_profile ?: '')
36 ],
37 'dpubmlstpy_loci': [
38 clihelp: 'The key name in the JSON response which lists the ' +
39 'allele URLs to download. ' +
40 " Default: ${params.dpubmlstpy_loci}",
41 cliflag: '-loci',
42 clivalue: (params.dpubmlstpy_loci ?: '')
43 ],
44 'dpubmlstpy_suffix': [
45 clihelp: 'What should be the suffix of the downloaded allele ' +
46 'FASTA. ' +
47 " Default: ${params.dpubmlstpy_suffix}",
48 cliflag: '-suffix',
49 clivalue: (params.dpubmlstpy_suffix ?: '')
50 ],
51 'dpubmlstpy_akey': [
52 clihelp: 'What is the key in the JSON response that contains ' +
53 'the URL for allele FASTA. ' +
54 " Default: ${params.dpubmlstpy_akey}",
55 cliflag: '-akey',
56 clivalue: (params.dpubmlstpy_akey ?: '')
57 ],
58 'dpubmlstpy_id': [
59 clihelp: 'What is the key in the JSON response that contains ' +
60 'the name of the allele FASTA. ' +
61 " Default: ${params.dpubmlstpy_id}",
62 cliflag: '-id',
63 clivalue: (params.dpubmlstpy_id ?: '')
64 ]
65 ]
66
67 toolspecs.each {
68 k, v -> tool.text['--' + k] = "${v.clihelp}"
69 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
70 }
71
72 return tool
73 }