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annotate 0.2.1/lib/help/flye.nf @ 34:4f9f145d1946

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 15:27:50 -0400
parents 77494b0fa3c7
children
rev   line source
kkonganti@0 1 // Help text for flye within CPIPES.
kkonganti@0 2
kkonganti@0 3 def flyeHelp(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 'flye_pacbio_raw': [
kkonganti@0 12 clihelp: 'Input FASTQ reads are PacBio regular CLR reads (<20% error) ' +
kkonganti@0 13 "Defaut: ${params.flye_pacbio_raw}",
kkonganti@0 14 cliflag: '--pacbio-raw',
kkonganti@0 15 clivalue: (params.flye_pacbio_raw ? ' ' : '')
kkonganti@0 16 ],
kkonganti@0 17 'flye_pacbio_corr': [
kkonganti@0 18 clihelp: 'Input FASTQ reads are PacBio reads that were corrected ' +
kkonganti@0 19 "with other methods (<3% error). Default: ${params.flye_pacbio_corr}",
kkonganti@0 20 cliflag: '--pacbio-corr',
kkonganti@0 21 clivalue: (params.flye_pacbio_corr ? ' ' : '')
kkonganti@0 22 ],
kkonganti@0 23 'flye_pacbio_hifi': [
kkonganti@0 24 clihelp: 'Input FASTQ reads are PacBio HiFi reads (<1% error). ' +
kkonganti@0 25 "Default: ${params.flye_pacbio_hifi}",
kkonganti@0 26 cliflag: '--pacbio-hifi',
kkonganti@0 27 clivalue: (params.flye_pacbio_hifi ? ' ' : '')
kkonganti@0 28 ],
kkonganti@0 29 'flye_nano_raw': [
kkonganti@0 30 clihelp: 'Input FASTQ reads are ONT regular reads, pre-Guppy5 (<20% error). ' +
kkonganti@0 31 "Default: ${params.flye_nano_raw}",
kkonganti@0 32 cliflag: '--nano-raw',
kkonganti@0 33 clivalue: (params.flye_nano_raw ? ' ' : '')
kkonganti@0 34 ],
kkonganti@0 35 'flye_nano_corr': [
kkonganti@0 36 clihelp: 'Input FASTQ reads are ONT reads that were corrected with other ' +
kkonganti@0 37 "methods (<3% error). Default: ${params.flye_nano_corr}",
kkonganti@0 38 cliflag: '--nano-corr',
kkonganti@0 39 clivalue: (params.flye_nano_corr ? ' ' : '')
kkonganti@0 40 ],
kkonganti@0 41 'flye_nano_hq': [
kkonganti@0 42 clihelp: 'Input FASTQ reads are ONT high-quality reads: ' +
kkonganti@0 43 "Guppy5+ SUP or Q20 (<5% error). Default: ${params.flye_nano_hq}",
kkonganti@0 44 cliflag: '--nano-hq',
kkonganti@0 45 clivalue: (params.flye_nano_hq ? ' ' : '')
kkonganti@0 46 ],
kkonganti@0 47 'flye_genome_size': [
kkonganti@0 48 clihelp: 'Estimated genome size (for example, 5m or 2.6g). ' +
kkonganti@0 49 "Default: ${params.flye_genome_size}",
kkonganti@0 50 cliflag: '--genome-size',
kkonganti@0 51 clivalue: (params.flye_genome_size ?: '')
kkonganti@0 52 ],
kkonganti@0 53 'flye_polish_iter': [
kkonganti@0 54 clihelp: 'Number of genome polishing iterations. ' +
kkonganti@0 55 "Default: ${params.flye_polish_iter}",
kkonganti@0 56 cliflag: '--iterations',
kkonganti@0 57 clivalue: (params.flye_polish_iter ?: '')
kkonganti@0 58 ],
kkonganti@0 59 'flye_meta': [
kkonganti@0 60 clihelp: "Do a metagenome assembly (unenven coverage mode). Default: ${params.flye_meta}",
kkonganti@0 61 cliflag: '--meta',
kkonganti@0 62 clivalue: (params.flye_meta ? ' ' : '')
kkonganti@0 63 ],
kkonganti@0 64 'flye_min_overlap': [
kkonganti@0 65 clihelp: "Minimum overlap between reads. Default: ${params.flye_min_overlap}",
kkonganti@0 66 cliflag: '--min-overlap',
kkonganti@0 67 clivalue: (params.flye_min_overlap ?: '')
kkonganti@0 68 ],
kkonganti@0 69 'flye_scaffold': [
kkonganti@0 70 clihelp: "Enable scaffolding using assembly graph. Default: ${params.flye_scaffold}",
kkonganti@0 71 cliflag: '--scaffold',
kkonganti@0 72 clivalue: (params.flye_scaffold ? ' ' : '')
kkonganti@0 73 ]
kkonganti@0 74 ]
kkonganti@0 75
kkonganti@0 76 toolspecs.each {
kkonganti@0 77 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0 78 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0 79 }
kkonganti@0 80
kkonganti@0 81 return tool
kkonganti@0 82 }