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comparison 0.2.0/lib/help/quast.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 quast within CPIPES.
2
3 def quastHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'quast_run': [
12 clihelp: 'Run quast tool. Default: ' +
13 (params.quast_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'quast_min_contig': [
18 clihelp: 'Lower threshold for contig length. ' +
19 "Default: ${params.quast_min_contig}",
20 cliflag: '-m',
21 clivalue: (params.quast_min_contig ?: '')
22 ],
23 'quast_split_scaffolds': [
24 clihelp: "Split assemblies by continuous fragments of N's" +
25 'and add such "contigs" to the comparison' +
26 "Default: ${params.quast_split_scaffolds}",
27 cliflag: '-s',
28 clivalue: (params.quast_split_scaffolds ? ' ' : '')
29 ],
30 'quast_euk': [
31 clihelp: 'Genome is eukaryotic (primarily affects gene prediction). ' +
32 "Default: ${params.quast_euk}",
33 cliflag: '-e',
34 clivalue: (params.quast_euk ? ' ' : '')
35 ],
36 'quast_fungal': [
37 clihelp: 'Genome is fungal (primarily affects gene prediction). ' +
38 "Default: ${params.quast_fungal}",
39 cliflag: '--fungal',
40 clivalue: (params.quast_fungal ? ' ' : '')
41 ],
42 'quast_large': [
43 clihelp: 'Use optimal parameters for evaluation of large genomes' +
44 "In particular, imposes '-e -m 3000 -i 500 -x 7000'." +
45 "Default: ${params.quast_large}",
46 cliflag: '--large',
47 clivalue: (params.quast_large ? ' ' : '')
48 ],
49 'quast_k': [
50 clihelp: 'Compute k-mer-based quality metrics (recommended for large genomes). ' +
51 "Default: ${params.quast_k}",
52 cliflag: '-k',
53 clivalue: (params.quast_k ? ' ' : '')
54 ],
55 'quast_kmer_size': [
56 clihelp: 'Size of k used in --quast_k. ' +
57 "Default: ${params.quast_kmer_size}",
58 cliflag: '--k-mer-size',
59 clivalue: (params.quast_kmer_size ?: 101)
60 ],
61 'quast_circos': [
62 clihelp: 'Draw circos plot. ' +
63 "Default: ${params.quast_circos}",
64 cliflag: '--circos',
65 clivalue: (params.quast_circos ? ' ' : '')
66 ],
67 'quast_glimmer': [
68 clihelp: 'Use GlimmerHMM for gene prediction. ' +
69 "Default: ${params.quast_glimmer}",
70 cliflag: '--glimmer',
71 clivalue: (params.quast_glimmer ? ' ' : '')
72 ],
73 'quast_gene_thr': [
74 clihelp: 'Comma-separated list of threshold lengths of genes to ' +
75 'search with Gene Finding module. ' +
76 "Default: ${params.quast_gene_thr}",
77 cliflag: '--gene-thresholds',
78 clivalue: (params.quast_gene_thr ?: '')
79 ],
80 'quast_rna_finding': [
81 clihelp: 'Predict ribosomal RNA genes using Barrnap. ' +
82 "Default: ${params.quast_rna_finding}",
83 cliflag: '--rna-finding',
84 clivalue: (params.quast_rna_finding ? ' ' : '')
85 ],
86 'quast_ref_size': [
87 clihelp: 'Estimated reference size in-case the reference genome is not supplied. ' +
88 "Default: ${params.quast_ref_size}",
89 cliflag: '--est-ref-size',
90 clivalue: (params.quast_ref_size ?: '')
91 ],
92 'quast_ctg_thr': [
93 clihelp: 'Comma-separated list of contig length thresholds. ' +
94 "Default: ${params.quast_ctg_thr}",
95 cliflag: '--contig-thresholds',
96 clivalue: (params.quast_ctg_thr ?: '')
97 ],
98 'quast_x_for_nx': [
99 clihelp: "Value of 'x' for Nx, Lx, etc metrics reported in addition to N50, L50, etc. " +
100 "Default: ${params.quast_x_for_nx}",
101 cliflag: '--x-for-Nx',
102 clivalue: (params.quast_x_for_nx ?: '')
103 ],
104 'quast_use_all_alns': [
105 clihelp: 'Compute genome fraction, # genes, # operons in QUAST v1.* style. ' +
106 "By default, QUAST filters Minimap's alignments to keep only best ones. " +
107 "Default: ${params.quast_glimmer}",
108 cliflag: '--use-all-alignments',
109 clivalue: (params.quast_use_all_alns ? ' ' : '')
110 ],
111 'quast_min_alignment': [
112 clihelp: 'The minimum alignment length. ' +
113 "Default: ${params.quast_min_alignment}",
114 cliflag: '-i',
115 clivalue: (params.quast_min_alignment ?: '')
116 ],
117 'quast_min_identity': [
118 clihelp: 'The minimum alignment identity (80.0, 100.0). ' +
119 "Default: ${params.quast_min_identity}",
120 cliflag: '--min-identity',
121 clivalue: (params.quast_min_identity ?: '')
122 ],
123 'quast_ambig_usage': [
124 clihelp: 'Use none, one, or all alignments of a contig when all of them. ' +
125 'are almost equally good (see --quast_ambig_score). ' +
126 "Default: ${params.quast_ambig_usage}",
127 cliflag: '-a',
128 clivalue: (params.quast_ambig_usage ?: '')
129 ],
130 'quast_ambig_score': [
131 clihelp: 'Score S for defining equally good alignments of a single contig. ' +
132 'All alignments are sorted by decreasing LEN * IDY% value. ' +
133 'All alignments with LEN * IDY% < S * best(LEN * IDY%) are ' +
134 'discarded. S should be between 0.8 and 1.0. ' +
135 "Default: ${params.quast_ambig_score}",
136 cliflag: '--ambiguity-score',
137 clivalue: (params.quast_ambig_score ?: '')
138 ],
139 'quast_strict_na': [
140 clihelp: 'Break contigs in any misassembly event when compute NAx and NGAx. '+
141 'By default, QUAST breaks contigs only by extensive misassemblies (not local ones). ' +
142 "Default: ${params.quast_strict_na}",
143 cliflag: '--strict-NA',
144 clivalue: (params.quast_strict_na ?: '')
145 ],
146 'quast_x': [
147 clihelp: 'Lower threshold for extensive misassembly size. All relocations with inconsistency ' +
148 'less than extensive-mis-size are counted as local misassemblies. ' +
149 "Default: ${params.quast_x}",
150 cliflag: '-x',
151 clivalue: (params.quast_x ?: '')
152 ],
153 'quast_local_mis_size': [
154 clihelp: 'Lower threshold on local misassembly size. Local misassemblies with inconsistency ' +
155 'less than local-mis-size are counted as (long) indels. ' +
156 "Default: ${params.quast_local_mis_size}",
157 cliflag: '--local-mis-size',
158 clivalue: (params.quast_local_mis_size ?: '')
159 ],
160 'quast_sca_gap_size': [
161 clihelp: 'Max allowed scaffold gap length difference. All relocations with inconsistency ' +
162 'less than scaffold-gap-size are counted as scaffold gap misassemblies. ' +
163 "Default: ${params.quast_sca_gap_size}",
164 cliflag: '--scaffold-gap-max-size',
165 clivalue: (params.quast_sca_gap_size ?: '')
166 ],
167 'quast_unaln_part_size': [
168 clihelp: 'Lower threshold for detecting partially unaligned contigs. Such contig should have ' +
169 'at least one unaligned fragment >= the threshold. ' +
170 "Default: ${params.quast_unaln_part_size}",
171 cliflag: '--unaligned-part-size',
172 clivalue: (params.quast_unaln_part_size ?: '')
173 ],
174 'quast_skip_unaln_mis_ctgs': [
175 clihelp: 'Do not distinguish contigs with >= 50% unaligned bases as a separate group ' +
176 'By default, QUAST does not count misassemblies in them. ' +
177 "Default: ${params.quast_skip_unaln_mis_ctgs}",
178 cliflag: '--skip-unaligned-mis-contigs',
179 clivalue: (params.quast_skip_unaln_mis_ctgs ?: '')
180 ],
181 'quast_fragmented': [
182 clihelp: 'Reference genome may be fragmented into small pieces (e.g. scaffolded reference). ' +
183 "Default: ${params.quast_fragmented}",
184 cliflag: '--fragmented',
185 clivalue: (params.quast_fragmented ? ' ' : '')
186 ],
187 'quast_frag_max_ident': [
188 clihelp: 'Mark translocation as fake if both alignments are located no further than N bases ' +
189 'from the ends of the reference fragments. ' +
190 "Default: ${params.quast_frag_max_ident}",
191 cliflag: '--fragmented-max-indent',
192 clivalue: (params.quast_frag_max_ident ?: '')
193 ],
194 'quast_plots_format': [
195 clihelp: 'Save plots in specified format [default: pdf]. ' +
196 'Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz' +
197 "Default: ${params.quast_plots_format}",
198 cliflag: '--plots-format',
199 clivalue: (params.quast_plots_format ?: '')
200 ],
201 ]
202
203 toolspecs.each {
204 k, v -> tool.text['--' + k] = "${v.clihelp}"
205 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
206 }
207
208 return tool
209 }