Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.5.0/lib/help/bbmerge.nf @ 15:1972677994a6

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"planemo upload"
author kkonganti
date Thu, 07 Sep 2023 10:27:12 -0400
parents 365849f031fd
children
rev   line source
kkonganti@1 1 // Help text for bbmerge within CPIPES.
kkonganti@1 2
kkonganti@1 3 def bbmergeHelp(params) {
kkonganti@1 4
kkonganti@1 5 Map tool = [:]
kkonganti@1 6 Map toolspecs = [:]
kkonganti@1 7 tool.text = [:]
kkonganti@1 8 tool.helpparams = [:]
kkonganti@1 9
kkonganti@1 10 toolspecs = [
kkonganti@1 11 'bbmerge_run': [
kkonganti@1 12 clihelp: 'Run BBMerge tool. Default: ' +
kkonganti@1 13 (params.bbmerge_run ?: false),
kkonganti@1 14 cliflag: null,
kkonganti@1 15 clivalue: null
kkonganti@1 16 ],
kkonganti@1 17 'bbmerge_reads': [
kkonganti@1 18 clihelp: 'Quit after this many read pairs (-1 means all) ' +
kkonganti@1 19 "Default: ${params.bbmerge_reads}",
kkonganti@1 20 cliflag: 'reads=',
kkonganti@1 21 clivalue: (params.bbmerge_reads ?: '')
kkonganti@1 22 ],
kkonganti@1 23 'bbmerge_adapters': [
kkonganti@1 24 clihelp: 'Absolute UNIX path pointing to the adapters file in ' +
kkonganti@1 25 "FASTA format. Default: ${params.bbmerge_adapters}",
kkonganti@1 26 cliflag: 'adapters=',
kkonganti@1 27 clivalue: (params.bbmerge_adapters ?: '')
kkonganti@1 28 ],
kkonganti@1 29 'bbmerge_ziplevel': [
kkonganti@1 30 clihelp: 'Set to 1 (lowest) through 9 (max) to change compression ' +
kkonganti@1 31 "level; lower compression is faster. Default: ${params.bbmerge_ziplevel}",
kkonganti@1 32 cliflag: 'ziplevel=',
kkonganti@1 33 clivalue: (params.bbmerge_ziplevel ?: '')
kkonganti@1 34 ],
kkonganti@1 35 'bbmerge_ordered': [
kkonganti@1 36 clihelp: 'Output reads in the same order as input. ' +
kkonganti@1 37 "Default: ${params.bbmerge_ordered}",
kkonganti@1 38 cliflag: 'ordered=',
kkonganti@1 39 clivalue: (params.bbmerge_ordered ?: '')
kkonganti@1 40 ],
kkonganti@1 41 'bbmerge_qtrim': [
kkonganti@1 42 clihelp: 'Trim read ends to remove bases with quality below --bbmerge_minq. ' +
kkonganti@1 43 'Trims BEFORE merging. Values: t (trim both ends), ' +
kkonganti@1 44 'f (neither end), r (right end only), l (left end only). ' +
kkonganti@1 45 "Default: ${params.bbmerge_qtrim}",
kkonganti@1 46 cliflag: 'qtrim=',
kkonganti@1 47 clivalue: (params.bbmerge_qtrim ?: '')
kkonganti@1 48 ],
kkonganti@1 49 'bbmerge_qtrim2': [
kkonganti@1 50 clihelp: 'May be specified instead of --bbmerge_qtrim to perform trimming ' +
kkonganti@1 51 'only if merging is unsuccesful. then retry merging. ' +
kkonganti@1 52 "Default: ${params.bbmerge_qtrim2}",
kkonganti@1 53 cliflag: 'qtrim2=',
kkonganti@1 54 clivalue: (params.bbmerge_qtrim2 ?: '')
kkonganti@1 55 ],
kkonganti@1 56 'bbmerge_trimq': [
kkonganti@1 57 clihelp: 'Trim quality threshold. This may be comma-delimited list (ascending) ' +
kkonganti@1 58 "to try multiple values. Default: ${params.bbmerge_trimq}",
kkonganti@1 59 cliflag: 'trimq=',
kkonganti@1 60 clivalue: (params.bbmerge_trimq ?: '')
kkonganti@1 61 ],
kkonganti@1 62 'bbmerge_minlength': [
kkonganti@1 63 clihelp: '(ml) Reads shorter than this after trimming, but before ' +
kkonganti@1 64 'merging, will be discarded. Pairs will be discarded only' +
kkonganti@1 65 "if both are shorter. Default: ${params.bbmerge_minlength}",
kkonganti@1 66 cliflag: 'minlength=',
kkonganti@1 67 clivalue: (params.bbmerge_minlength ?: '')
kkonganti@1 68 ],
kkonganti@1 69 'bbmerge_tbo': [
kkonganti@1 70 clihelp: '(trimbyoverlap). Trim overlapping reads to remove right ' +
kkonganti@1 71 "most (3') non-overlaping portion instead of joining " +
kkonganti@1 72 "Default: ${params.bbmerge_tbo}",
kkonganti@1 73 cliflag: 'tbo=',
kkonganti@1 74 clivalue: (params.bbmerge_tbo ?: '')
kkonganti@1 75 ],
kkonganti@1 76 'bbmerge_minavgquality': [
kkonganti@1 77 clihelp: '(maq). Reads with average quality below this after trimming will ' +
kkonganti@1 78 "not be attempted to merge. Default: ${params.bbmerge_minavgquality}",
kkonganti@1 79 cliflag: 'minavgquality=',
kkonganti@1 80 clivalue: (params.bbmerge_minavgquality ?: '')
kkonganti@1 81 ],
kkonganti@1 82 'bbmerge_trimpolya': [
kkonganti@1 83 clihelp: 'Trim trailing poly-A tail from adapter output. Only affects ' +
kkonganti@1 84 'outadapter. This also trims poly-A followed by poly-G, which ' +
kkonganti@1 85 "occurs on NextSeq. Default: ${params.bbmerge_trimpolya}",
kkonganti@1 86 cliflag: 'trimpolya=',
kkonganti@1 87 clivalue: (params.bbmerge_trimpolya ?: '')
kkonganti@1 88 ],
kkonganti@1 89 'bbmerge_pfilter': [
kkonganti@1 90 clihelp: 'Ban improbable overlaps. Higher is more strict. 0 will ' +
kkonganti@1 91 'disable the filter; 1 will allow only perfect overlaps. ' +
kkonganti@1 92 "Default: ${params.bbmerge_pfilter}",
kkonganti@1 93 cliflag: 'pfilter=',
kkonganti@1 94 clivalue: (params.bbmerge_pfilter ?: '')
kkonganti@1 95 ],
kkonganti@1 96 'bbmerge_ouq': [
kkonganti@1 97 clihelp: 'Calculate best overlap using quality values. ' +
kkonganti@1 98 "Default: ${params.bbmerge_ouq}",
kkonganti@1 99 cliflag: 'ouq',
kkonganti@1 100 clivalue: (params.bbmerge_ouq ?: '')
kkonganti@1 101 ],
kkonganti@1 102 'bbmerge_owq': [
kkonganti@1 103 clihelp: 'Calculate best overlap without using quality values. ' +
kkonganti@1 104 "Default: ${params.bbmerge_owq}",
kkonganti@1 105 cliflag: 'owq=',
kkonganti@1 106 clivalue: (params.bbmerge_owq ?: '')
kkonganti@1 107 ],
kkonganti@1 108 'bbmerge_strict': [
kkonganti@1 109 clihelp: 'Decrease false positive rate and merging rate. ' +
kkonganti@1 110 "Default: ${params.bbmerge_strict}",
kkonganti@1 111 cliflag: 'strict=',
kkonganti@1 112 clivalue: (params.bbmerge_strict ?: '')
kkonganti@1 113 ],
kkonganti@1 114 'bbmerge_verystrict': [
kkonganti@1 115 clihelp: 'Greatly decrease false positive rate and merging rate. ' +
kkonganti@1 116 "Default: ${params.bbmerge_verystrict}",
kkonganti@1 117 cliflag: 'verystrict=',
kkonganti@1 118 clivalue: (params.bbmerge_verystrict ?: '')
kkonganti@1 119 ],
kkonganti@1 120 'bbmerge_ultrastrict': [
kkonganti@1 121 clihelp: 'Decrease false positive rate and merging rate even more. ' +
kkonganti@1 122 "Default: ${params.bbmerge_ultrastrict}",
kkonganti@1 123 cliflag: 'ultrastrict=',
kkonganti@1 124 clivalue: (params.bbmerge_ultrastrict ?: '')
kkonganti@1 125 ],
kkonganti@1 126 'bbmerge_maxstrict': [
kkonganti@1 127 clihelp: 'Maxiamally decrease false positive rate and merging rate. ' +
kkonganti@1 128 "Default: ${params.bbmerge_maxstrict}",
kkonganti@1 129 cliflag: 'maxstrict=',
kkonganti@1 130 clivalue: (params.bbmerge_maxstrict ?: '')
kkonganti@1 131 ],
kkonganti@1 132 'bbmerge_loose': [
kkonganti@1 133 clihelp: 'Increase false positive rate and merging rate. ' +
kkonganti@1 134 "Default: ${params.bbmerge_loose}",
kkonganti@1 135 cliflag: 'loose=',
kkonganti@1 136 clivalue: (params.bbmerge_loose ?: '')
kkonganti@1 137 ],
kkonganti@1 138 'bbmerge_veryloose': [
kkonganti@1 139 clihelp: 'Greatly increase false positive rate and merging rate. ' +
kkonganti@1 140 "Default: ${params.bbmerge_veryloose}",
kkonganti@1 141 cliflag: 'veryloose=',
kkonganti@1 142 clivalue: (params.bbmerge_veryloose ?: '')
kkonganti@1 143 ],
kkonganti@1 144 'bbmerge_ultraloose': [
kkonganti@1 145 clihelp: 'Increase false positive rate and merging rate even more. ' +
kkonganti@1 146 "Default: ${params.bbmerge_ultraloose}",
kkonganti@1 147 cliflag: 'ultraloose=',
kkonganti@1 148 clivalue: (params.bbmerge_ultraloose ?: '')
kkonganti@1 149 ],
kkonganti@1 150 'bbmerge_maxloose': [
kkonganti@1 151 clihelp: 'Maximally increase false positive rate and merging rate. ' +
kkonganti@1 152 "Default: ${params.bbmerge_maxloose}",
kkonganti@1 153 cliflag: 'maxloose=',
kkonganti@1 154 clivalue: (params.bbmerge_maxloose ?: '')
kkonganti@1 155 ],
kkonganti@1 156 'bbmerge_fast': [
kkonganti@1 157 clihelp: 'Fastest possible preset. ' +
kkonganti@1 158 "Default: ${params.bbmerge_fast}",
kkonganti@1 159 cliflag: 'fast=',
kkonganti@1 160 clivalue: (params.bbmerge_fast ?: '')
kkonganti@1 161 ],
kkonganti@1 162 'bbmerge_k': [
kkonganti@1 163 clihelp: 'Kmer length. 31 (or less) is fastest and uses the least ' +
kkonganti@1 164 'memory, but higher values may be more accurate. ' +
kkonganti@1 165 '60 tends to work well for 150bp reads. ' +
kkonganti@1 166 "Default: ${params.bbmerge_k}",
kkonganti@1 167 cliflag: 'k=',
kkonganti@1 168 clivalue: (params.bbmerge_k ?: '')
kkonganti@1 169 ],
kkonganti@1 170 'bbmerge_prealloc': [
kkonganti@1 171 clihelp: 'Pre-allocate memory rather than dynamically growing. ' +
kkonganti@1 172 'Faster and more memory-efficient for large datasets. ' +
kkonganti@1 173 'A float fraction (0-1) may be specified, default 1. ' +
kkonganti@1 174 "Default: ${params.bbmerge_prealloc}",
kkonganti@1 175 cliflag: 'prealloc=',
kkonganti@1 176 clivalue: (params.bbmerge_prealloc ?: '')
kkonganti@1 177 ]
kkonganti@1 178 ]
kkonganti@1 179
kkonganti@1 180 toolspecs.each {
kkonganti@1 181 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@1 182 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@1 183 }
kkonganti@1 184
kkonganti@1 185 return tool
kkonganti@1 186 }