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annotate 0.4.0/lib/help/flye.nf @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 // Help text for flye within CPIPES.
kkonganti@101 2
kkonganti@101 3 def flyeHelp(params) {
kkonganti@101 4
kkonganti@101 5 Map tool = [:]
kkonganti@101 6 Map toolspecs = [:]
kkonganti@101 7 tool.text = [:]
kkonganti@101 8 tool.helpparams = [:]
kkonganti@101 9
kkonganti@101 10 toolspecs = [
kkonganti@101 11 'flye_pacbio_raw': [
kkonganti@101 12 clihelp: 'Input FASTQ reads are PacBio regular CLR reads (<20% error) ' +
kkonganti@101 13 "Defaut: ${params.flye_pacbio_raw}",
kkonganti@101 14 cliflag: '--pacbio-raw',
kkonganti@101 15 clivalue: (params.flye_pacbio_raw ? ' ' : '')
kkonganti@101 16 ],
kkonganti@101 17 'flye_pacbio_corr': [
kkonganti@101 18 clihelp: 'Input FASTQ reads are PacBio reads that were corrected ' +
kkonganti@101 19 "with other methods (<3% error). Default: ${params.flye_pacbio_corr}",
kkonganti@101 20 cliflag: '--pacbio-corr',
kkonganti@101 21 clivalue: (params.flye_pacbio_corr ? ' ' : '')
kkonganti@101 22 ],
kkonganti@101 23 'flye_pacbio_hifi': [
kkonganti@101 24 clihelp: 'Input FASTQ reads are PacBio HiFi reads (<1% error). ' +
kkonganti@101 25 "Default: ${params.flye_pacbio_hifi}",
kkonganti@101 26 cliflag: '--pacbio-hifi',
kkonganti@101 27 clivalue: (params.flye_pacbio_hifi ? ' ' : '')
kkonganti@101 28 ],
kkonganti@101 29 'flye_nano_raw': [
kkonganti@101 30 clihelp: 'Input FASTQ reads are ONT regular reads, pre-Guppy5 (<20% error). ' +
kkonganti@101 31 "Default: ${params.flye_nano_raw}",
kkonganti@101 32 cliflag: '--nano-raw',
kkonganti@101 33 clivalue: (params.flye_nano_raw ? ' ' : '')
kkonganti@101 34 ],
kkonganti@101 35 'flye_nano_corr': [
kkonganti@101 36 clihelp: 'Input FASTQ reads are ONT reads that were corrected with other ' +
kkonganti@101 37 "methods (<3% error). Default: ${params.flye_nano_corr}",
kkonganti@101 38 cliflag: '--nano-corr',
kkonganti@101 39 clivalue: (params.flye_nano_corr ? ' ' : '')
kkonganti@101 40 ],
kkonganti@101 41 'flye_nano_hq': [
kkonganti@101 42 clihelp: 'Input FASTQ reads are ONT high-quality reads: ' +
kkonganti@101 43 "Guppy5+ SUP or Q20 (<5% error). Default: ${params.flye_nano_hq}",
kkonganti@101 44 cliflag: '--nano-hq',
kkonganti@101 45 clivalue: (params.flye_nano_hq ? ' ' : '')
kkonganti@101 46 ],
kkonganti@101 47 'flye_genome_size': [
kkonganti@101 48 clihelp: 'Estimated genome size (for example, 5m or 2.6g). ' +
kkonganti@101 49 "Default: ${params.flye_genome_size}",
kkonganti@101 50 cliflag: '--genome-size',
kkonganti@101 51 clivalue: (params.flye_genome_size ?: '')
kkonganti@101 52 ],
kkonganti@101 53 'flye_polish_iter': [
kkonganti@101 54 clihelp: 'Number of genome polishing iterations. ' +
kkonganti@101 55 "Default: ${params.flye_polish_iter}",
kkonganti@101 56 cliflag: '--iterations',
kkonganti@101 57 clivalue: (params.flye_polish_iter ?: '')
kkonganti@101 58 ],
kkonganti@101 59 'flye_meta': [
kkonganti@101 60 clihelp: "Do a metagenome assembly (unenven coverage mode). Default: ${params.flye_meta}",
kkonganti@101 61 cliflag: '--meta',
kkonganti@101 62 clivalue: (params.flye_meta ? ' ' : '')
kkonganti@101 63 ],
kkonganti@101 64 'flye_min_overlap': [
kkonganti@101 65 clihelp: "Minimum overlap between reads. Default: ${params.flye_min_overlap}",
kkonganti@101 66 cliflag: '--min-overlap',
kkonganti@101 67 clivalue: (params.flye_min_overlap ?: '')
kkonganti@101 68 ],
kkonganti@101 69 'flye_scaffold': [
kkonganti@101 70 clihelp: "Enable scaffolding using assembly graph. Default: ${params.flye_scaffold}",
kkonganti@101 71 cliflag: '--scaffold',
kkonganti@101 72 clivalue: (params.flye_scaffold ? ' ' : '')
kkonganti@101 73 ]
kkonganti@101 74 ]
kkonganti@101 75
kkonganti@101 76 toolspecs.each {
kkonganti@101 77 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@101 78 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@101 79 }
kkonganti@101 80
kkonganti@101 81 return tool
kkonganti@101 82 }