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annotate 0.1.0/lib/help/quast.nf @ 6:a3c1cba6f773

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 19:52:20 -0500
parents c8597e9e1a97
children
rev   line source
kkonganti@0 1 // Help text for quast within CPIPES.
kkonganti@0 2
kkonganti@0 3 def quastHelp(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 'quast_run': [
kkonganti@0 12 clihelp: 'Run quast tool. Default: ' +
kkonganti@0 13 (params.quast_run ?: false),
kkonganti@0 14 cliflag: null,
kkonganti@0 15 clivalue: null
kkonganti@0 16 ],
kkonganti@0 17 'quast_min_contig': [
kkonganti@0 18 clihelp: 'Lower threshold for contig length. ' +
kkonganti@0 19 "Default: ${params.quast_min_contig}",
kkonganti@0 20 cliflag: '-m',
kkonganti@0 21 clivalue: (params.quast_min_contig ?: '')
kkonganti@0 22 ],
kkonganti@0 23 'quast_split_scaffolds': [
kkonganti@0 24 clihelp: "Split assemblies by continuous fragments of N's" +
kkonganti@0 25 'and add such "contigs" to the comparison' +
kkonganti@0 26 "Default: ${params.quast_split_scaffolds}",
kkonganti@0 27 cliflag: '-s',
kkonganti@0 28 clivalue: (params.quast_split_scaffolds ? ' ' : '')
kkonganti@0 29 ],
kkonganti@0 30 'quast_euk': [
kkonganti@0 31 clihelp: 'Genome is eukaryotic (primarily affects gene prediction). ' +
kkonganti@0 32 "Default: ${params.quast_euk}",
kkonganti@0 33 cliflag: '-e',
kkonganti@0 34 clivalue: (params.quast_euk ? ' ' : '')
kkonganti@0 35 ],
kkonganti@0 36 'quast_fungal': [
kkonganti@0 37 clihelp: 'Genome is fungal (primarily affects gene prediction). ' +
kkonganti@0 38 "Default: ${params.quast_fungal}",
kkonganti@0 39 cliflag: '--fungal',
kkonganti@0 40 clivalue: (params.quast_fungal ? ' ' : '')
kkonganti@0 41 ],
kkonganti@0 42 'quast_large': [
kkonganti@0 43 clihelp: 'Use optimal parameters for evaluation of large genomes' +
kkonganti@0 44 "In particular, imposes '-e -m 3000 -i 500 -x 7000'." +
kkonganti@0 45 "Default: ${params.quast_large}",
kkonganti@0 46 cliflag: '--large',
kkonganti@0 47 clivalue: (params.quast_large ? ' ' : '')
kkonganti@0 48 ],
kkonganti@0 49 'quast_k': [
kkonganti@0 50 clihelp: 'Compute k-mer-based quality metrics (recommended for large genomes). ' +
kkonganti@0 51 "Default: ${params.quast_k}",
kkonganti@0 52 cliflag: '-k',
kkonganti@0 53 clivalue: (params.quast_k ? ' ' : '')
kkonganti@0 54 ],
kkonganti@0 55 'quast_kmer_size': [
kkonganti@0 56 clihelp: 'Size of k used in --quast_k. ' +
kkonganti@0 57 "Default: ${params.quast_kmer_size}",
kkonganti@0 58 cliflag: '--k-mer-size',
kkonganti@0 59 clivalue: (params.quast_kmer_size ?: 101)
kkonganti@0 60 ],
kkonganti@0 61 'quast_circos': [
kkonganti@0 62 clihelp: 'Draw circos plot. ' +
kkonganti@0 63 "Default: ${params.quast_circos}",
kkonganti@0 64 cliflag: '--circos',
kkonganti@0 65 clivalue: (params.quast_circos ? ' ' : '')
kkonganti@0 66 ],
kkonganti@0 67 'quast_glimmer': [
kkonganti@0 68 clihelp: 'Use GlimmerHMM for gene prediction. ' +
kkonganti@0 69 "Default: ${params.quast_glimmer}",
kkonganti@0 70 cliflag: '--glimmer',
kkonganti@0 71 clivalue: (params.quast_glimmer ? ' ' : '')
kkonganti@0 72 ],
kkonganti@0 73 'quast_gene_thr': [
kkonganti@0 74 clihelp: 'Comma-separated list of threshold lengths of genes to ' +
kkonganti@0 75 'search with Gene Finding module. ' +
kkonganti@0 76 "Default: ${params.quast_gene_thr}",
kkonganti@0 77 cliflag: '--gene-thresholds',
kkonganti@0 78 clivalue: (params.quast_gene_thr ?: '')
kkonganti@0 79 ],
kkonganti@0 80 'quast_rna_finding': [
kkonganti@0 81 clihelp: 'Predict ribosomal RNA genes using Barrnap. ' +
kkonganti@0 82 "Default: ${params.quast_rna_finding}",
kkonganti@0 83 cliflag: '--rna-finding',
kkonganti@0 84 clivalue: (params.quast_rna_finding ? ' ' : '')
kkonganti@0 85 ],
kkonganti@0 86 'quast_ref_size': [
kkonganti@0 87 clihelp: 'Estimated reference size in-case the reference genome is not supplied. ' +
kkonganti@0 88 "Default: ${params.quast_ref_size}",
kkonganti@0 89 cliflag: '--est-ref-size',
kkonganti@0 90 clivalue: (params.quast_ref_size ?: '')
kkonganti@0 91 ],
kkonganti@0 92 'quast_ctg_thr': [
kkonganti@0 93 clihelp: 'Comma-separated list of contig length thresholds. ' +
kkonganti@0 94 "Default: ${params.quast_ctg_thr}",
kkonganti@0 95 cliflag: '--contig-thresholds',
kkonganti@0 96 clivalue: (params.quast_ctg_thr ?: '')
kkonganti@0 97 ],
kkonganti@0 98 'quast_x_for_nx': [
kkonganti@0 99 clihelp: "Value of 'x' for Nx, Lx, etc metrics reported in addition to N50, L50, etc. " +
kkonganti@0 100 "Default: ${params.quast_x_for_nx}",
kkonganti@0 101 cliflag: '--x-for-Nx',
kkonganti@0 102 clivalue: (params.quast_x_for_nx ?: '')
kkonganti@0 103 ],
kkonganti@0 104 'quast_use_all_alns': [
kkonganti@0 105 clihelp: 'Compute genome fraction, # genes, # operons in QUAST v1.* style. ' +
kkonganti@0 106 "By default, QUAST filters Minimap's alignments to keep only best ones. " +
kkonganti@0 107 "Default: ${params.quast_glimmer}",
kkonganti@0 108 cliflag: '--use-all-alignments',
kkonganti@0 109 clivalue: (params.quast_use_all_alns ? ' ' : '')
kkonganti@0 110 ],
kkonganti@0 111 'quast_min_alignment': [
kkonganti@0 112 clihelp: 'The minimum alignment length. ' +
kkonganti@0 113 "Default: ${params.quast_min_alignment}",
kkonganti@0 114 cliflag: '-i',
kkonganti@0 115 clivalue: (params.quast_min_alignment ?: '')
kkonganti@0 116 ],
kkonganti@0 117 'quast_min_identity': [
kkonganti@0 118 clihelp: 'The minimum alignment identity (80.0, 100.0). ' +
kkonganti@0 119 "Default: ${params.quast_min_identity}",
kkonganti@0 120 cliflag: '--min-identity',
kkonganti@0 121 clivalue: (params.quast_min_identity ?: '')
kkonganti@0 122 ],
kkonganti@0 123 'quast_ambig_usage': [
kkonganti@0 124 clihelp: 'Use none, one, or all alignments of a contig when all of them. ' +
kkonganti@0 125 'are almost equally good (see --quast_ambig_score). ' +
kkonganti@0 126 "Default: ${params.quast_ambig_usage}",
kkonganti@0 127 cliflag: '-a',
kkonganti@0 128 clivalue: (params.quast_ambig_usage ?: '')
kkonganti@0 129 ],
kkonganti@0 130 'quast_ambig_score': [
kkonganti@0 131 clihelp: 'Score S for defining equally good alignments of a single contig. ' +
kkonganti@0 132 'All alignments are sorted by decreasing LEN * IDY% value. ' +
kkonganti@0 133 'All alignments with LEN * IDY% < S * best(LEN * IDY%) are ' +
kkonganti@0 134 'discarded. S should be between 0.8 and 1.0. ' +
kkonganti@0 135 "Default: ${params.quast_ambig_score}",
kkonganti@0 136 cliflag: '--ambiguity-score',
kkonganti@0 137 clivalue: (params.quast_ambig_score ?: '')
kkonganti@0 138 ],
kkonganti@0 139 'quast_strict_na': [
kkonganti@0 140 clihelp: 'Break contigs in any misassembly event when compute NAx and NGAx. '+
kkonganti@0 141 'By default, QUAST breaks contigs only by extensive misassemblies (not local ones). ' +
kkonganti@0 142 "Default: ${params.quast_strict_na}",
kkonganti@0 143 cliflag: '--strict-NA',
kkonganti@0 144 clivalue: (params.quast_strict_na ?: '')
kkonganti@0 145 ],
kkonganti@0 146 'quast_x': [
kkonganti@0 147 clihelp: 'Lower threshold for extensive misassembly size. All relocations with inconsistency ' +
kkonganti@0 148 'less than extensive-mis-size are counted as local misassemblies. ' +
kkonganti@0 149 "Default: ${params.quast_x}",
kkonganti@0 150 cliflag: '-x',
kkonganti@0 151 clivalue: (params.quast_x ?: '')
kkonganti@0 152 ],
kkonganti@0 153 'quast_local_mis_size': [
kkonganti@0 154 clihelp: 'Lower threshold on local misassembly size. Local misassemblies with inconsistency ' +
kkonganti@0 155 'less than local-mis-size are counted as (long) indels. ' +
kkonganti@0 156 "Default: ${params.quast_local_mis_size}",
kkonganti@0 157 cliflag: '--local-mis-size',
kkonganti@0 158 clivalue: (params.quast_local_mis_size ?: '')
kkonganti@0 159 ],
kkonganti@0 160 'quast_sca_gap_size': [
kkonganti@0 161 clihelp: 'Max allowed scaffold gap length difference. All relocations with inconsistency ' +
kkonganti@0 162 'less than scaffold-gap-size are counted as scaffold gap misassemblies. ' +
kkonganti@0 163 "Default: ${params.quast_sca_gap_size}",
kkonganti@0 164 cliflag: '--scaffold-gap-max-size',
kkonganti@0 165 clivalue: (params.quast_sca_gap_size ?: '')
kkonganti@0 166 ],
kkonganti@0 167 'quast_unaln_part_size': [
kkonganti@0 168 clihelp: 'Lower threshold for detecting partially unaligned contigs. Such contig should have ' +
kkonganti@0 169 'at least one unaligned fragment >= the threshold. ' +
kkonganti@0 170 "Default: ${params.quast_unaln_part_size}",
kkonganti@0 171 cliflag: '--unaligned-part-size',
kkonganti@0 172 clivalue: (params.quast_unaln_part_size ?: '')
kkonganti@0 173 ],
kkonganti@0 174 'quast_skip_unaln_mis_ctgs': [
kkonganti@0 175 clihelp: 'Do not distinguish contigs with >= 50% unaligned bases as a separate group ' +
kkonganti@0 176 'By default, QUAST does not count misassemblies in them. ' +
kkonganti@0 177 "Default: ${params.quast_skip_unaln_mis_ctgs}",
kkonganti@0 178 cliflag: '--skip-unaligned-mis-contigs',
kkonganti@0 179 clivalue: (params.quast_skip_unaln_mis_ctgs ?: '')
kkonganti@0 180 ],
kkonganti@0 181 'quast_fragmented': [
kkonganti@0 182 clihelp: 'Reference genome may be fragmented into small pieces (e.g. scaffolded reference). ' +
kkonganti@0 183 "Default: ${params.quast_fragmented}",
kkonganti@0 184 cliflag: '--fragmented',
kkonganti@0 185 clivalue: (params.quast_fragmented ? ' ' : '')
kkonganti@0 186 ],
kkonganti@0 187 'quast_frag_max_ident': [
kkonganti@0 188 clihelp: 'Mark translocation as fake if both alignments are located no further than N bases ' +
kkonganti@0 189 'from the ends of the reference fragments. ' +
kkonganti@0 190 "Default: ${params.quast_frag_max_ident}",
kkonganti@0 191 cliflag: '--fragmented-max-indent',
kkonganti@0 192 clivalue: (params.quast_frag_max_ident ?: '')
kkonganti@0 193 ],
kkonganti@0 194 'quast_plots_format': [
kkonganti@0 195 clihelp: 'Save plots in specified format [default: pdf]. ' +
kkonganti@0 196 'Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz' +
kkonganti@0 197 "Default: ${params.quast_plots_format}",
kkonganti@0 198 cliflag: '--plots-format',
kkonganti@0 199 clivalue: (params.quast_plots_format ?: '')
kkonganti@0 200 ],
kkonganti@0 201 ]
kkonganti@0 202
kkonganti@0 203 toolspecs.each {
kkonganti@0 204 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0 205 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0 206 }
kkonganti@0 207
kkonganti@0 208 return tool
kkonganti@0 209 }