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annotate 0.1.0/lib/help/bbmerge.nf @ 7:f02f143c02fb

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 20:24:38 -0500
parents c8597e9e1a97
children
rev   line source
kkonganti@0 1 // Help text for bbmerge within CPIPES.
kkonganti@0 2
kkonganti@0 3 def bbmergeHelp(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 'bbmerge_run': [
kkonganti@0 12 clihelp: 'Run BBMerge tool. Default: ' +
kkonganti@0 13 (params.bbmerge_run ?: false),
kkonganti@0 14 cliflag: null,
kkonganti@0 15 clivalue: null
kkonganti@0 16 ],
kkonganti@0 17 'bbmerge_reads': [
kkonganti@0 18 clihelp: 'Quit after this many read pairs (-1 means all) ' +
kkonganti@0 19 <<<<<<< HEAD
kkonganti@0 20 "Defaut: ${params.bbmerge_reads}",
kkonganti@0 21 =======
kkonganti@0 22 "Default: ${params.bbmerge_reads}",
kkonganti@0 23 >>>>>>> 0.5.0
kkonganti@0 24 cliflag: 'reads=',
kkonganti@0 25 clivalue: (params.bbmerge_reads ?: '')
kkonganti@0 26 ],
kkonganti@0 27 'bbmerge_adapters': [
kkonganti@0 28 clihelp: 'Absolute UNIX path pointing to the adapters file in ' +
kkonganti@0 29 <<<<<<< HEAD
kkonganti@0 30 "FASTA format. Defaut: ${params.bbmerge_adapters}",
kkonganti@0 31 =======
kkonganti@0 32 "FASTA format. Default: ${params.bbmerge_adapters}",
kkonganti@0 33 >>>>>>> 0.5.0
kkonganti@0 34 cliflag: 'adapters=',
kkonganti@0 35 clivalue: (params.bbmerge_adapters ?: '')
kkonganti@0 36 ],
kkonganti@0 37 'bbmerge_ziplevel': [
kkonganti@0 38 clihelp: 'Set to 1 (lowest) through 9 (max) to change compression ' +
kkonganti@0 39 "level; lower compression is faster. Default: ${params.bbmerge_ziplevel}",
kkonganti@0 40 cliflag: 'ziplevel=',
kkonganti@0 41 clivalue: (params.bbmerge_ziplevel ?: '')
kkonganti@0 42 ],
kkonganti@0 43 'bbmerge_ordered': [
kkonganti@0 44 clihelp: 'Output reads in the same order as input. ' +
kkonganti@0 45 "Default: ${params.bbmerge_ordered}",
kkonganti@0 46 cliflag: 'ordered=',
kkonganti@0 47 clivalue: (params.bbmerge_ordered ?: '')
kkonganti@0 48 ],
kkonganti@0 49 'bbmerge_qtrim': [
kkonganti@0 50 clihelp: 'Trim read ends to remove bases with quality below --bbmerge_minq. ' +
kkonganti@0 51 'Trims BEFORE merging. Values: t (trim both ends), ' +
kkonganti@0 52 'f (neither end), r (right end only), l (left end only). ' +
kkonganti@0 53 "Default: ${params.bbmerge_qtrim}",
kkonganti@0 54 cliflag: 'qtrim=',
kkonganti@0 55 clivalue: (params.bbmerge_qtrim ?: '')
kkonganti@0 56 ],
kkonganti@0 57 'bbmerge_qtrim2': [
kkonganti@0 58 clihelp: 'May be specified instead of --bbmerge_qtrim to perform trimming ' +
kkonganti@0 59 'only if merging is unsuccesful. then retry merging. ' +
kkonganti@0 60 "Default: ${params.bbmerge_qtrim2}",
kkonganti@0 61 cliflag: 'qtrim2=',
kkonganti@0 62 clivalue: (params.bbmerge_qtrim2 ?: '')
kkonganti@0 63 ],
kkonganti@0 64 'bbmerge_trimq': [
kkonganti@0 65 clihelp: 'Trim quality threshold. This may be comma-delimited list (ascending) ' +
kkonganti@0 66 "to try multiple values. Default: ${params.bbmerge_trimq}",
kkonganti@0 67 cliflag: 'trimq=',
kkonganti@0 68 clivalue: (params.bbmerge_trimq ?: '')
kkonganti@0 69 ],
kkonganti@0 70 'bbmerge_minlength': [
kkonganti@0 71 clihelp: '(ml) Reads shorter than this after trimming, but before ' +
kkonganti@0 72 'merging, will be discarded. Pairs will be discarded only' +
kkonganti@0 73 "if both are shorter. Default: ${params.bbmerge_minlength}",
kkonganti@0 74 cliflag: 'minlength=',
kkonganti@0 75 clivalue: (params.bbmerge_minlength ?: '')
kkonganti@0 76 ],
kkonganti@0 77 'bbmerge_tbo': [
kkonganti@0 78 clihelp: '(trimbyoverlap). Trim overlapping reads to remove right ' +
kkonganti@0 79 "most (3') non-overlaping portion instead of joining " +
kkonganti@0 80 "Default: ${params.bbmerge_tbo}",
kkonganti@0 81 cliflag: 'tbo=',
kkonganti@0 82 clivalue: (params.bbmerge_tbo ?: '')
kkonganti@0 83 ],
kkonganti@0 84 'bbmerge_minavgquality': [
kkonganti@0 85 clihelp: '(maq). Reads with average quality below this after trimming will ' +
kkonganti@0 86 "not be attempted to merge. Default: ${params.bbmerge_minavgquality}",
kkonganti@0 87 cliflag: 'minavgquality=',
kkonganti@0 88 clivalue: (params.bbmerge_minavgquality ?: '')
kkonganti@0 89 ],
kkonganti@0 90 'bbmerge_trimpolya': [
kkonganti@0 91 clihelp: 'Trim trailing poly-A tail from adapter output. Only affects ' +
kkonganti@0 92 'outadapter. This also trims poly-A followed by poly-G, which ' +
kkonganti@0 93 "occurs on NextSeq. Default: ${params.bbmerge_trimpolya}",
kkonganti@0 94 cliflag: 'trimpolya=',
kkonganti@0 95 clivalue: (params.bbmerge_trimpolya ?: '')
kkonganti@0 96 ],
kkonganti@0 97 'bbmerge_pfilter': [
kkonganti@0 98 clihelp: 'Ban improbable overlaps. Higher is more strict. 0 will ' +
kkonganti@0 99 'disable the filter; 1 will allow only perfect overlaps. ' +
kkonganti@0 100 "Default: ${params.bbmerge_pfilter}",
kkonganti@0 101 cliflag: 'pfilter=',
kkonganti@0 102 clivalue: (params.bbmerge_pfilter ?: '')
kkonganti@0 103 ],
kkonganti@0 104 'bbmerge_ouq': [
kkonganti@0 105 clihelp: 'Calculate best overlap using quality values. ' +
kkonganti@0 106 "Default: ${params.bbmerge_ouq}",
kkonganti@0 107 cliflag: 'ouq',
kkonganti@0 108 clivalue: (params.bbmerge_ouq ?: '')
kkonganti@0 109 ],
kkonganti@0 110 'bbmerge_owq': [
kkonganti@0 111 clihelp: 'Calculate best overlap without using quality values. ' +
kkonganti@0 112 "Default: ${params.bbmerge_owq}",
kkonganti@0 113 cliflag: 'owq=',
kkonganti@0 114 clivalue: (params.bbmerge_owq ?: '')
kkonganti@0 115 ],
kkonganti@0 116 'bbmerge_strict': [
kkonganti@0 117 clihelp: 'Decrease false positive rate and merging rate. ' +
kkonganti@0 118 "Default: ${params.bbmerge_strict}",
kkonganti@0 119 cliflag: 'strict=',
kkonganti@0 120 clivalue: (params.bbmerge_strict ?: '')
kkonganti@0 121 ],
kkonganti@0 122 'bbmerge_verystrict': [
kkonganti@0 123 clihelp: 'Greatly decrease false positive rate and merging rate. ' +
kkonganti@0 124 "Default: ${params.bbmerge_verystrict}",
kkonganti@0 125 cliflag: 'verystrict=',
kkonganti@0 126 clivalue: (params.bbmerge_verystrict ?: '')
kkonganti@0 127 ],
kkonganti@0 128 'bbmerge_ultrastrict': [
kkonganti@0 129 clihelp: 'Decrease false positive rate and merging rate even more. ' +
kkonganti@0 130 "Default: ${params.bbmerge_ultrastrict}",
kkonganti@0 131 cliflag: 'ultrastrict=',
kkonganti@0 132 clivalue: (params.bbmerge_ultrastrict ?: '')
kkonganti@0 133 ],
kkonganti@0 134 'bbmerge_maxstrict': [
kkonganti@0 135 clihelp: 'Maxiamally decrease false positive rate and merging rate. ' +
kkonganti@0 136 "Default: ${params.bbmerge_maxstrict}",
kkonganti@0 137 cliflag: 'maxstrict=',
kkonganti@0 138 clivalue: (params.bbmerge_maxstrict ?: '')
kkonganti@0 139 ],
kkonganti@0 140 'bbmerge_loose': [
kkonganti@0 141 clihelp: 'Increase false positive rate and merging rate. ' +
kkonganti@0 142 "Default: ${params.bbmerge_loose}",
kkonganti@0 143 cliflag: 'loose=',
kkonganti@0 144 clivalue: (params.bbmerge_loose ?: '')
kkonganti@0 145 ],
kkonganti@0 146 'bbmerge_veryloose': [
kkonganti@0 147 clihelp: 'Greatly increase false positive rate and merging rate. ' +
kkonganti@0 148 "Default: ${params.bbmerge_veryloose}",
kkonganti@0 149 cliflag: 'veryloose=',
kkonganti@0 150 clivalue: (params.bbmerge_veryloose ?: '')
kkonganti@0 151 ],
kkonganti@0 152 'bbmerge_ultraloose': [
kkonganti@0 153 clihelp: 'Increase false positive rate and merging rate even more. ' +
kkonganti@0 154 "Default: ${params.bbmerge_ultraloose}",
kkonganti@0 155 cliflag: 'ultraloose=',
kkonganti@0 156 clivalue: (params.bbmerge_ultraloose ?: '')
kkonganti@0 157 ],
kkonganti@0 158 'bbmerge_maxloose': [
kkonganti@0 159 clihelp: 'Maximally increase false positive rate and merging rate. ' +
kkonganti@0 160 "Default: ${params.bbmerge_maxloose}",
kkonganti@0 161 cliflag: 'maxloose=',
kkonganti@0 162 clivalue: (params.bbmerge_maxloose ?: '')
kkonganti@0 163 ],
kkonganti@0 164 'bbmerge_fast': [
kkonganti@0 165 clihelp: 'Fastest possible preset. ' +
kkonganti@0 166 "Default: ${params.bbmerge_fast}",
kkonganti@0 167 cliflag: 'fast=',
kkonganti@0 168 clivalue: (params.bbmerge_fast ?: '')
kkonganti@0 169 ],
kkonganti@0 170 'bbmerge_k': [
kkonganti@0 171 clihelp: 'Kmer length. 31 (or less) is fastest and uses the least ' +
kkonganti@0 172 'memory, but higher values may be more accurate. ' +
kkonganti@0 173 '60 tends to work well for 150bp reads. ' +
kkonganti@0 174 "Default: ${params.bbmerge_k}",
kkonganti@0 175 cliflag: 'k=',
kkonganti@0 176 clivalue: (params.bbmerge_k ?: '')
kkonganti@0 177 ],
kkonganti@0 178 'bbmerge_prealloc': [
kkonganti@0 179 clihelp: 'Pre-allocate memory rather than dynamically growing. ' +
kkonganti@0 180 'Faster and more memory-efficient for large datasets. ' +
kkonganti@0 181 'A float fraction (0-1) may be specified, default 1. ' +
kkonganti@0 182 "Default: ${params.bbmerge_prealloc}",
kkonganti@0 183 cliflag: 'prealloc=',
kkonganti@0 184 clivalue: (params.bbmerge_prealloc ?: '')
kkonganti@0 185 ]
kkonganti@0 186 ]
kkonganti@0 187
kkonganti@0 188 toolspecs.each {
kkonganti@0 189 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0 190 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0 191 }
kkonganti@0 192
kkonganti@0 193 return tool
kkonganti@0 194 }