Mercurial > repos > kkonganti > cfsan_cronology
diff 0.1.0/lib/help/quast.nf @ 0:c8597e9e1a97
"planemo upload"
author | kkonganti |
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date | Mon, 27 Nov 2023 12:37:44 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.1.0/lib/help/quast.nf Mon Nov 27 12:37:44 2023 -0500 @@ -0,0 +1,209 @@ +// Help text for quast within CPIPES. + +def quastHelp(params) { + + Map tool = [:] + Map toolspecs = [:] + tool.text = [:] + tool.helpparams = [:] + + toolspecs = [ + 'quast_run': [ + clihelp: 'Run quast tool. Default: ' + + (params.quast_run ?: false), + cliflag: null, + clivalue: null + ], + 'quast_min_contig': [ + clihelp: 'Lower threshold for contig length. ' + + "Default: ${params.quast_min_contig}", + cliflag: '-m', + clivalue: (params.quast_min_contig ?: '') + ], + 'quast_split_scaffolds': [ + clihelp: "Split assemblies by continuous fragments of N's" + + 'and add such "contigs" to the comparison' + + "Default: ${params.quast_split_scaffolds}", + cliflag: '-s', + clivalue: (params.quast_split_scaffolds ? ' ' : '') + ], + 'quast_euk': [ + clihelp: 'Genome is eukaryotic (primarily affects gene prediction). ' + + "Default: ${params.quast_euk}", + cliflag: '-e', + clivalue: (params.quast_euk ? ' ' : '') + ], + 'quast_fungal': [ + clihelp: 'Genome is fungal (primarily affects gene prediction). ' + + "Default: ${params.quast_fungal}", + cliflag: '--fungal', + clivalue: (params.quast_fungal ? ' ' : '') + ], + 'quast_large': [ + clihelp: 'Use optimal parameters for evaluation of large genomes' + + "In particular, imposes '-e -m 3000 -i 500 -x 7000'." + + "Default: ${params.quast_large}", + cliflag: '--large', + clivalue: (params.quast_large ? ' ' : '') + ], + 'quast_k': [ + clihelp: 'Compute k-mer-based quality metrics (recommended for large genomes). ' + + "Default: ${params.quast_k}", + cliflag: '-k', + clivalue: (params.quast_k ? ' ' : '') + ], + 'quast_kmer_size': [ + clihelp: 'Size of k used in --quast_k. ' + + "Default: ${params.quast_kmer_size}", + cliflag: '--k-mer-size', + clivalue: (params.quast_kmer_size ?: 101) + ], + 'quast_circos': [ + clihelp: 'Draw circos plot. ' + + "Default: ${params.quast_circos}", + cliflag: '--circos', + clivalue: (params.quast_circos ? ' ' : '') + ], + 'quast_glimmer': [ + clihelp: 'Use GlimmerHMM for gene prediction. ' + + "Default: ${params.quast_glimmer}", + cliflag: '--glimmer', + clivalue: (params.quast_glimmer ? ' ' : '') + ], + 'quast_gene_thr': [ + clihelp: 'Comma-separated list of threshold lengths of genes to ' + + 'search with Gene Finding module. ' + + "Default: ${params.quast_gene_thr}", + cliflag: '--gene-thresholds', + clivalue: (params.quast_gene_thr ?: '') + ], + 'quast_rna_finding': [ + clihelp: 'Predict ribosomal RNA genes using Barrnap. ' + + "Default: ${params.quast_rna_finding}", + cliflag: '--rna-finding', + clivalue: (params.quast_rna_finding ? ' ' : '') + ], + 'quast_ref_size': [ + clihelp: 'Estimated reference size in-case the reference genome is not supplied. ' + + "Default: ${params.quast_ref_size}", + cliflag: '--est-ref-size', + clivalue: (params.quast_ref_size ?: '') + ], + 'quast_ctg_thr': [ + clihelp: 'Comma-separated list of contig length thresholds. ' + + "Default: ${params.quast_ctg_thr}", + cliflag: '--contig-thresholds', + clivalue: (params.quast_ctg_thr ?: '') + ], + 'quast_x_for_nx': [ + clihelp: "Value of 'x' for Nx, Lx, etc metrics reported in addition to N50, L50, etc. " + + "Default: ${params.quast_x_for_nx}", + cliflag: '--x-for-Nx', + clivalue: (params.quast_x_for_nx ?: '') + ], + 'quast_use_all_alns': [ + clihelp: 'Compute genome fraction, # genes, # operons in QUAST v1.* style. ' + + "By default, QUAST filters Minimap's alignments to keep only best ones. " + + "Default: ${params.quast_glimmer}", + cliflag: '--use-all-alignments', + clivalue: (params.quast_use_all_alns ? ' ' : '') + ], + 'quast_min_alignment': [ + clihelp: 'The minimum alignment length. ' + + "Default: ${params.quast_min_alignment}", + cliflag: '-i', + clivalue: (params.quast_min_alignment ?: '') + ], + 'quast_min_identity': [ + clihelp: 'The minimum alignment identity (80.0, 100.0). ' + + "Default: ${params.quast_min_identity}", + cliflag: '--min-identity', + clivalue: (params.quast_min_identity ?: '') + ], + 'quast_ambig_usage': [ + clihelp: 'Use none, one, or all alignments of a contig when all of them. ' + + 'are almost equally good (see --quast_ambig_score). ' + + "Default: ${params.quast_ambig_usage}", + cliflag: '-a', + clivalue: (params.quast_ambig_usage ?: '') + ], + 'quast_ambig_score': [ + clihelp: 'Score S for defining equally good alignments of a single contig. ' + + 'All alignments are sorted by decreasing LEN * IDY% value. ' + + 'All alignments with LEN * IDY% < S * best(LEN * IDY%) are ' + + 'discarded. S should be between 0.8 and 1.0. ' + + "Default: ${params.quast_ambig_score}", + cliflag: '--ambiguity-score', + clivalue: (params.quast_ambig_score ?: '') + ], + 'quast_strict_na': [ + clihelp: 'Break contigs in any misassembly event when compute NAx and NGAx. '+ + 'By default, QUAST breaks contigs only by extensive misassemblies (not local ones). ' + + "Default: ${params.quast_strict_na}", + cliflag: '--strict-NA', + clivalue: (params.quast_strict_na ?: '') + ], + 'quast_x': [ + clihelp: 'Lower threshold for extensive misassembly size. All relocations with inconsistency ' + + 'less than extensive-mis-size are counted as local misassemblies. ' + + "Default: ${params.quast_x}", + cliflag: '-x', + clivalue: (params.quast_x ?: '') + ], + 'quast_local_mis_size': [ + clihelp: 'Lower threshold on local misassembly size. Local misassemblies with inconsistency ' + + 'less than local-mis-size are counted as (long) indels. ' + + "Default: ${params.quast_local_mis_size}", + cliflag: '--local-mis-size', + clivalue: (params.quast_local_mis_size ?: '') + ], + 'quast_sca_gap_size': [ + clihelp: 'Max allowed scaffold gap length difference. All relocations with inconsistency ' + + 'less than scaffold-gap-size are counted as scaffold gap misassemblies. ' + + "Default: ${params.quast_sca_gap_size}", + cliflag: '--scaffold-gap-max-size', + clivalue: (params.quast_sca_gap_size ?: '') + ], + 'quast_unaln_part_size': [ + clihelp: 'Lower threshold for detecting partially unaligned contigs. Such contig should have ' + + 'at least one unaligned fragment >= the threshold. ' + + "Default: ${params.quast_unaln_part_size}", + cliflag: '--unaligned-part-size', + clivalue: (params.quast_unaln_part_size ?: '') + ], + 'quast_skip_unaln_mis_ctgs': [ + clihelp: 'Do not distinguish contigs with >= 50% unaligned bases as a separate group ' + + 'By default, QUAST does not count misassemblies in them. ' + + "Default: ${params.quast_skip_unaln_mis_ctgs}", + cliflag: '--skip-unaligned-mis-contigs', + clivalue: (params.quast_skip_unaln_mis_ctgs ?: '') + ], + 'quast_fragmented': [ + clihelp: 'Reference genome may be fragmented into small pieces (e.g. scaffolded reference). ' + + "Default: ${params.quast_fragmented}", + cliflag: '--fragmented', + clivalue: (params.quast_fragmented ? ' ' : '') + ], + 'quast_frag_max_ident': [ + clihelp: 'Mark translocation as fake if both alignments are located no further than N bases ' + + 'from the ends of the reference fragments. ' + + "Default: ${params.quast_frag_max_ident}", + cliflag: '--fragmented-max-indent', + clivalue: (params.quast_frag_max_ident ?: '') + ], + 'quast_plots_format': [ + clihelp: 'Save plots in specified format [default: pdf]. ' + + 'Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz' + + "Default: ${params.quast_plots_format}", + cliflag: '--plots-format', + clivalue: (params.quast_plots_format ?: '') + ], + ] + + toolspecs.each { + k, v -> tool.text['--' + k] = "${v.clihelp}" + tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] + } + + return tool +} \ No newline at end of file