|
kkonganti@0
|
1 // Help text for get_top_unique_mash_hit_genomes.py (tuspy) within CPIPES.
|
|
kkonganti@0
|
2
|
|
kkonganti@0
|
3 def tuspyHelp(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 'tuspy_run': [
|
|
kkonganti@0
|
12 clihelp: 'Run the get_top_unique_mash_hits_genomes.py ' +
|
|
kkonganti@0
|
13 'script. Default: ' +
|
|
kkonganti@0
|
14 (params.tuspy_run ?: false),
|
|
kkonganti@0
|
15 cliflag: null,
|
|
kkonganti@0
|
16 clivalue: null
|
|
kkonganti@0
|
17 ],
|
|
kkonganti@0
|
18 'tuspy_s': [
|
|
kkonganti@0
|
19 clihelp: 'Absolute UNIX path to metadata text file with the ' +
|
|
kkonganti@0
|
20 'field separator, | and ' +
|
|
kkonganti@0
|
21 '5 fields: serotype|asm_lvl|asm_url|snp_cluster_id' +
|
|
kkonganti@0
|
22 'Ex: serotype=Derby,antigen_formula=4:f,g:-|Scaffold|402440|ftp://...' +
|
|
kkonganti@0
|
23 '|PDS000096654.2. Mentioning this option will create a pickle file for the ' +
|
|
kkonganti@0
|
24 'provided metadata and exits.' +
|
|
kkonganti@0
|
25 " Default: ${params.tuspy_s}",
|
|
kkonganti@0
|
26 cliflag: '-s',
|
|
kkonganti@0
|
27 clivalue: (params.tuspy_s ?: '')
|
|
kkonganti@0
|
28 ],
|
|
kkonganti@0
|
29 'tuspy_m': [
|
|
kkonganti@0
|
30 clihelp: 'Absolute UNIX path to mash screen results file.' +
|
|
kkonganti@0
|
31 " Default: ${params.tuspy_m}",
|
|
kkonganti@0
|
32 cliflag: '-m',
|
|
kkonganti@0
|
33 clivalue: (params.tuspy_m ?: '')
|
|
kkonganti@0
|
34 ],
|
|
kkonganti@0
|
35 'tuspy_ps': [
|
|
kkonganti@0
|
36 clihelp: 'Absolute UNIX Path to serialized metadata object ' +
|
|
kkonganti@0
|
37 'in a pickle file.' +
|
|
kkonganti@0
|
38 " Default: ${params.tuspy_ps}",
|
|
kkonganti@0
|
39 cliflag: '-ps',
|
|
kkonganti@0
|
40 clivalue: (params.tuspy_ps ?: '')
|
|
kkonganti@0
|
41 ],
|
|
kkonganti@0
|
42 'tuspy_gd': [
|
|
kkonganti@0
|
43 clihelp: 'Absolute UNIX Path to directory containing ' +
|
|
kkonganti@0
|
44 'gzipped genome FASTA files.' +
|
|
kkonganti@0
|
45 " Default: ${params.tuspy_gd}",
|
|
kkonganti@0
|
46 cliflag: '-gd',
|
|
kkonganti@0
|
47 clivalue: (params.tuspy_gd ?: '')
|
|
kkonganti@0
|
48 ],
|
|
kkonganti@0
|
49 'tuspy_gds': [
|
|
kkonganti@0
|
50 clihelp: 'Genome FASTA file suffix to search for in the ' +
|
|
kkonganti@0
|
51 'genome directory.' +
|
|
kkonganti@0
|
52 " Default: ${params.tuspy_gds}",
|
|
kkonganti@0
|
53 cliflag: '-gds',
|
|
kkonganti@0
|
54 clivalue: (params.tuspy_gds ?: '')
|
|
kkonganti@0
|
55 ],
|
|
kkonganti@0
|
56 'tuspy_n': [
|
|
kkonganti@0
|
57 clihelp: 'Return up to this many number of top N unique ' +
|
|
kkonganti@0
|
58 'genome accession hits.' +
|
|
kkonganti@0
|
59 " Default: ${params.tuspy_n}",
|
|
kkonganti@0
|
60 cliflag: '-n',
|
|
kkonganti@0
|
61 clivalue: (params.tuspy_n ?: '')
|
|
kkonganti@0
|
62 ]
|
|
kkonganti@0
|
63 ]
|
|
kkonganti@0
|
64
|
|
kkonganti@0
|
65 toolspecs.each {
|
|
kkonganti@0
|
66 k, v -> tool.text['--' + k] = "${v.clihelp}"
|
|
kkonganti@0
|
67 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
|
|
kkonganti@0
|
68 }
|
|
kkonganti@0
|
69
|
|
kkonganti@0
|
70 return tool
|
|
kkonganti@0
|
71 } |
