Mercurial > repos > kkonganti > cfsan_cronology
comparison 0.2.0/lib/help/guncrun.nf @ 11:a5f31c44f8c9
planemo upload
author | kkonganti |
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date | Mon, 15 Jul 2024 16:11:44 -0400 |
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10:ddf7a172bf30 | 11:a5f31c44f8c9 |
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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 } |