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comparison 0.2.0/lib/help/guncrun.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 gunc run within CPIPES.
2
3 def guncrunHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'guncrun_run': [
12 clihelp: 'Run `gunc run` tool. Default: ' +
13 (params.guncrun_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'guncrun_in_is_fasta': [
18 clihelp: 'Is input a file in FASTA format. ' +
19 "Default: ${params.guncrun_in_is_fasta}",
20 cliflag: null,
21 clivalue: null
22 ],
23 'guncrun_in_is_fofn': [
24 clihelp: 'Is input a file of file names. ' +
25 "Default: ${params.guncrun_in_is_fofn}",
26 cliflag: null,
27 clivalue: null
28 ],
29 'guncrun_in_is_dir': [
30 clihelp: 'Is input a directory of FASTA files. ' +
31 "Default: ${params.guncrun_in_is_dir}",
32 cliflag: null,
33 clivalue: null
34 ],
35 'guncrun_file_suffix': [
36 clihelp: "Suffix of files if input is a directory. " +
37 "Default: ${params.guncrun_file_suffix}",
38 cliflag: '--file_suffix',
39 clivalue: (params.guncrun_file_suffix ?: '')
40 ],
41 'guncrun_gene_calls': [
42 clihelp: 'Input files are in FASTA faa format. ' +
43 "Default: ${params.guncrun_gene_calls}",
44 cliflag: '--gene_calls',
45 clivalue: (params.guncrun_gene_calls ? ' ' : '')
46 ],
47 'guncrun_temp_dir': [
48 clihelp: 'Path to directory to store temp files. ' +
49 "Default: ${params.guncrun_temp_dir}",
50 cliflag: '--temp_dir',
51 clivalue: (params.guncrun_temp_dir ?: '')
52 ],
53 'guncrun_sensitive': [
54 clihelp: 'Run with high sensitivity. ' +
55 "Default: ${params.guncrun_sensitive}",
56 cliflag: '--sensitive',
57 clivalue: (params.guncrun_sensitive ? ' ' : '')
58 ],
59 'guncrun_detailed_output': [
60 clihelp: 'Output scores for every taxa level. ' +
61 "Default: ${params.guncrun_detailed_output}",
62 cliflag: '--detailed_output',
63 clivalue: (params.guncrun_detailed_output ? ' ' : '')
64 ],
65 'guncrun_ctg_tax_output': [
66 clihelp: 'Output assignments for each contig. ' +
67 "Default: ${params.guncrun_ctg_tax_output}",
68 cliflag: '--contig_taxonomy_output',
69 clivalue: (params.guncrun_ctg_tax_output ? ' ' : '')
70 ],
71 'guncrun_use_species_lvl': [
72 clihelp: 'Allow species level to be picked as maxCSS. ' +
73 "Default: ${params.guncrun_use_species_lvl}",
74 cliflag: '--use_species_level',
75 clivalue: (params.guncrun_use_species_lvl ? ' ' : '')
76 ],
77 'guncrun_min_mapped_genes': [
78 clihelp: 'Do not calculate GUNC score if number of mapped ' +
79 'genes is below this value. ' +
80 "Default: ${params.guncrun_min_mapped_genes}",
81 cliflag: '--min_mapped_genes',
82 clivalue: (params.guncrun_min_mapped_genes ?: '')
83 ]
84 ]
85
86 toolspecs.each {
87 k, v -> tool.text['--' + k] = "${v.clihelp}"
88 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
89 }
90
91 return tool
92 }