|
kkonganti@0
|
1 // Help text for dl_pubmlst_profiles_and_schemes.py (dpubmlstpy) within CPIPES.
|
|
kkonganti@0
|
2
|
|
kkonganti@0
|
3 def dpubmlstpyHelp(params) {
|
|
kkonganti@0
|
4
|
|
kkonganti@0
|
5 Map tool = [:]
|
|
kkonganti@0
|
6 Map toolspecs = [:]
|
|
kkonganti@0
|
7 tool.text = [:]
|
|
kkonganti@0
|
8 tool.helpparams = [:]
|
|
kkonganti@0
|
9
|
|
kkonganti@0
|
10 toolspecs = [
|
|
kkonganti@0
|
11 'dpubmlstpy_run': [
|
|
kkonganti@0
|
12 clihelp: 'Run the dl_pubmlst_profiles_and_schemes.py ' +
|
|
kkonganti@0
|
13 'script. Default: ' +
|
|
kkonganti@0
|
14 (params.dpubmlstpy_run ?: false),
|
|
kkonganti@0
|
15 cliflag: null,
|
|
kkonganti@0
|
16 clivalue: null
|
|
kkonganti@0
|
17 ],
|
|
kkonganti@0
|
18 'dpubmlstpy_org': [
|
|
kkonganti@0
|
19 clihelp: 'The organism name to download the MLST alleles ' +
|
|
kkonganti@0
|
20 'FASTA and profile CSV for. ' +
|
|
kkonganti@0
|
21 " Default: ${params.dpubmlstpy_org}",
|
|
kkonganti@0
|
22 cliflag: '-org',
|
|
kkonganti@0
|
23 clivalue: (params.dpubmlstpy_org ?: '')
|
|
kkonganti@0
|
24 ],
|
|
kkonganti@0
|
25 'dpubmlstpy_mlsts': [
|
|
kkonganti@0
|
26 clihelp: 'The MLST scheme ID to download. ' +
|
|
kkonganti@0
|
27 " Default: ${params.dpubmlstpy_mlsts}",
|
|
kkonganti@0
|
28 cliflag: '-mlsts',
|
|
kkonganti@0
|
29 clivalue: (params.dpubmlstpy_mlsts ?: '')
|
|
kkonganti@0
|
30 ],
|
|
kkonganti@0
|
31 'dpubmlstpy_profile': [
|
|
kkonganti@0
|
32 clihelp: 'The MLST profile name in the scheme. ' +
|
|
kkonganti@0
|
33 " Default: ${params.dpubmlstpy_profile}",
|
|
kkonganti@0
|
34 cliflag: '-profile',
|
|
kkonganti@0
|
35 clivalue: (params.dpubmlstpy_profile ?: '')
|
|
kkonganti@0
|
36 ],
|
|
kkonganti@0
|
37 'dpubmlstpy_loci': [
|
|
kkonganti@0
|
38 clihelp: 'The key name in the JSON response which lists the ' +
|
|
kkonganti@0
|
39 'allele URLs to download. ' +
|
|
kkonganti@0
|
40 " Default: ${params.dpubmlstpy_loci}",
|
|
kkonganti@0
|
41 cliflag: '-loci',
|
|
kkonganti@0
|
42 clivalue: (params.dpubmlstpy_loci ?: '')
|
|
kkonganti@0
|
43 ],
|
|
kkonganti@0
|
44 'dpubmlstpy_suffix': [
|
|
kkonganti@0
|
45 clihelp: 'What should be the suffix of the downloaded allele ' +
|
|
kkonganti@0
|
46 'FASTA. ' +
|
|
kkonganti@0
|
47 " Default: ${params.dpubmlstpy_suffix}",
|
|
kkonganti@0
|
48 cliflag: '-suffix',
|
|
kkonganti@0
|
49 clivalue: (params.dpubmlstpy_suffix ?: '')
|
|
kkonganti@0
|
50 ],
|
|
kkonganti@0
|
51 'dpubmlstpy_akey': [
|
|
kkonganti@0
|
52 clihelp: 'What is the key in the JSON response that contains ' +
|
|
kkonganti@0
|
53 'the URL for allele FASTA. ' +
|
|
kkonganti@0
|
54 " Default: ${params.dpubmlstpy_akey}",
|
|
kkonganti@0
|
55 cliflag: '-akey',
|
|
kkonganti@0
|
56 clivalue: (params.dpubmlstpy_akey ?: '')
|
|
kkonganti@0
|
57 ],
|
|
kkonganti@0
|
58 'dpubmlstpy_id': [
|
|
kkonganti@0
|
59 clihelp: 'What is the key in the JSON response that contains ' +
|
|
kkonganti@0
|
60 'the name of the allele FASTA. ' +
|
|
kkonganti@0
|
61 " Default: ${params.dpubmlstpy_id}",
|
|
kkonganti@0
|
62 cliflag: '-id',
|
|
kkonganti@0
|
63 clivalue: (params.dpubmlstpy_id ?: '')
|
|
kkonganti@0
|
64 ]
|
|
kkonganti@0
|
65 ]
|
|
kkonganti@0
|
66
|
|
kkonganti@0
|
67 toolspecs.each {
|
|
kkonganti@0
|
68 k, v -> tool.text['--' + k] = "${v.clihelp}"
|
|
kkonganti@0
|
69 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
|
|
kkonganti@0
|
70 }
|
|
kkonganti@0
|
71
|
|
kkonganti@0
|
72 return tool
|
|
kkonganti@0
|
73 } |
