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comparison 0.2.0/lib/help/prokka.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 prokka within CPIPES.
2
3 def prokkaHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'prokka_run': [
12 clihelp: 'Run prokka tool. Default: ' +
13 (params.prokka_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'prokka_dbdir': [
18 clihelp: 'Path to prokka database root folder. ' +
19 "Default: ${params.prokka_dbdir}",
20 cliflag: '--dbdir',
21 clivalue: (params.prokka_dbdir ?: '')
22 ],
23 'prokka_addgenes': [
24 clihelp: "Add 'gene' features for each 'CDS' feature. " +
25 "Default: ${params.prokka_addgenes}",
26 cliflag: '--addgenes',
27 clivalue: (params.prokka_addgenes ? ' ' : '')
28 ],
29 'prokka_addmrna': [
30 clihelp: "Add 'mRNA' features for each 'CDS' feature. " +
31 "Default: ${params.prokka_addmrna}",
32 cliflag: '--addmrna',
33 clivalue: (params.prokka_addmrna ? ' ' : '')
34 ],
35 'prokka_locustag': [
36 clihelp: "Locus tag prefix. " +
37 "Default: ${params.prokka_locustag}",
38 cliflag: '--locustag',
39 clivalue: (params.prokka_locustag ?: '')
40 ],
41 'prokka_increment': [
42 clihelp: "Locus tag counter increment. " +
43 "Default: ${params.prokka_increment}",
44 cliflag: '--increment',
45 clivalue: (params.prokka_increment ?: '')
46 ],
47 'prokka_gffver': [
48 clihelp: 'GFF version. ' +
49 "Default: ${params.prokka_gffver}",
50 cliflag: '-gffver',
51 clivalue: (params.prokka_gffver ?: '')
52 ],
53 'prokka_compliant': [
54 clihelp: ' Force Genbank/ENA/DDJB compliance i.e. ' +
55 '--prokka_addgenes --prokka_mincontiglen 200 --prokka_centre XXX. ' +
56 "Default: ${params.prokka_compliant}",
57 cliflag: '--compliant',
58 clivalue: (params.prokka_compliant ? ' ' : '')
59 ],
60 'prokka_centre': [
61 clihelp: 'Sequencing centre ID. ' +
62 "Default: ${params.prokka_centre}",
63 cliflag: '--centre',
64 clivalue: (params.prokka_centre ?: '')
65 ],
66 'prokka_accver': [
67 clihelp: 'Version to put in GenBank file. ' +
68 "Default: ${params.prokka_accver}",
69 cliflag: '--accver',
70 clivalue: (params.prokka_accver ?: '')
71 ],
72 'prokka_genus': [
73 clihelp: 'Genus name. ' +
74 "Default: ${params.prokka_genus}",
75 cliflag: '--genus',
76 clivalue: (params.prokka_genus ?: '')
77 ],
78 'prokka_species': [
79 clihelp: 'Species name. ' +
80 "Default: ${params.prokka_species}",
81 cliflag: '--species',
82 clivalue: (params.prokka_species ?: '')
83 ],
84 'prokka_strain': [
85 clihelp: 'Strain name. ' +
86 "Default: ${params.prokka_strain}",
87 cliflag: '--strain',
88 clivalue: (params.prokka_strain ?: '')
89 ],
90 'prokka_plasmid': [
91 clihelp: 'Plasmid name or identifier. ' +
92 "Default: ${params.prokka_plasmid}",
93 cliflag: '--plasmid',
94 clivalue: (params.prokka_plasmid ?: '')
95 ],
96 'prokka_kingdom': [
97 clihelp: 'Annotation mode: Archaea|Bacteria|Mitochondria|Viruses. ' +
98 "Default: ${params.prokka_kingdom}",
99 cliflag: '--kingdom',
100 clivalue: (params.prokka_kingdom ?: '')
101 ],
102 'prokka_gcode': [
103 clihelp: 'Genetic code / Translation table (set if --prokka_kingdom is set). ' +
104 "Default: ${params.prokka_gcode}",
105 cliflag: '--gcode',
106 clivalue: (params.prokka_gcode ?: '')
107 ],
108 'prokka_usegenus': [
109 clihelp: 'Use genus-specific BLAST databases (needs --prokka_genus) ' +
110 "Default: ${params.prokka_usegenus}",
111 cliflag: '--usegenus',
112 clivalue: (params.prokka_usegenus ? ' ' : '')
113 ],
114 'prokka_metagenome': [
115 clihelp: 'Improve gene predictions for highly fragmented genomes. ' +
116 "Default: ${params.prokka_metagenome}",
117 cliflag: '--metagenome',
118 clivalue: (params.prokka_metagenome ? ' ' : '')
119 ],
120 'prokka_rawproduct': [
121 clihelp: 'Version to put in GenBank file. ' +
122 "Default: ${params.prokka_rawproduct}",
123 cliflag: '--rawproduct',
124 clivalue: (params.prokka_rawproduct ?: '')
125 ],
126 'prokka_cdsrnaolap': [
127 clihelp: 'Do not clean up /product annotation. ' +
128 "Default: ${params.prokka_cdsrnaolap}",
129 cliflag: '--cdsrnaolap',
130 clivalue: (params.prokka_cdsrnaolap ? ' ' : '')
131 ],
132 'prokka_evalue': [
133 clihelp: 'Similarity e-value cut-off. ' +
134 "Default: ${params.prokka_evalue}",
135 cliflag: '--evalue',
136 clivalue: (params.prokka_evalue ?: '')
137 ],
138 'prokka_coverage': [
139 clihelp: 'Minimum coverage on query protein. ' +
140 "Default: ${params.prokka_coverage}",
141 cliflag: '--coverage',
142 clivalue: (params.prokka_coverage ?: '')
143 ],
144 'prokka_fast': [
145 clihelp: 'Fast mode - only use basic BLASTP databases. ' +
146 "Default: ${params.prokka_fast}",
147 cliflag: '--fast',
148 clivalue: (params.prokka_fast ? ' ' : '')
149 ],
150 'prokka_noanno': [
151 clihelp: 'For CDS just set /product="unannotated protein". ' +
152 "Default: ${params.prokka_noanno}",
153 cliflag: '--noanno',
154 clivalue: (params.prokka_noanno ? ' ' : '')
155 ],
156 'prokka_mincontiglen': [
157 clihelp: 'Minimum contig size [NCBI needs 200]. ' +
158 "Default: ${params.prokka_mincontiglen}",
159 cliflag: '--mincontiglen',
160 clivalue: (params.prokka_mincontiglen ?: '')
161 ],
162 'prokka_rfam': [
163 clihelp: 'Enable searching for ncRNAs with Infernal+Rfam (SLOW!). ' +
164 "Default: ${params.prokka_rfam}",
165 cliflag: '--rfam',
166 clivalue: (params.prokka_rfam ? ' ' : '')
167 ],
168 'prokka_norrna': [
169 clihelp: "Don't run rRNA search. " +
170 "Default: ${params.prokka_norrna}",
171 cliflag: '--norrna',
172 clivalue: (params.prokka_norrna ? ' ' : '')
173 ],
174 'prokka_notrna': [
175 clihelp: "Don't run tRNA search. " +
176 "Default: ${params.prokka_notrna}",
177 cliflag: '--notrna',
178 clivalue: (params.prokka_notrna ? ' ' : '')
179 ],
180 'prokka_rnammer': [
181 clihelp: 'Prefer RNAmmer over Barrnap for rRNA prediction. ' +
182 "Default: ${params.prokka_rnammer}",
183 cliflag: '--rnammer',
184 clivalue: (params.prokka_rnammer ? ' ' : '')
185 ]
186 ]
187
188 toolspecs.each {
189 k, v -> tool.text['--' + k] = "${v.clihelp}"
190 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
191 }
192
193 return tool
194 }