kkonganti@11: // Help text for bbmerge within CPIPES.
kkonganti@11: 
kkonganti@11: def bbmergeHelp(params) {
kkonganti@11: 
kkonganti@11:     Map tool = [:]
kkonganti@11:     Map toolspecs = [:]
kkonganti@11:     tool.text = [:]
kkonganti@11:     tool.helpparams = [:]
kkonganti@11: 
kkonganti@11:     toolspecs = [
kkonganti@11:         'bbmerge_run': [
kkonganti@11:             clihelp: 'Run BBMerge tool. Default: ' +
kkonganti@11:                 (params.bbmerge_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'bbmerge_reads': [
kkonganti@11:             clihelp: 'Quit after this many read pairs (-1 means all) ' +
kkonganti@11:                 "Default: ${params.bbmerge_reads}",
kkonganti@11:             cliflag: 'reads=',
kkonganti@11:             clivalue: (params.bbmerge_reads ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_adapters': [
kkonganti@11:             clihelp: 'Absolute UNIX path pointing to the adapters file in ' +
kkonganti@11:                 "FASTA format. Default: ${params.bbmerge_adapters}",
kkonganti@11:             cliflag: 'adapters=',
kkonganti@11:             clivalue: (params.bbmerge_adapters ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_ziplevel': [
kkonganti@11:             clihelp: 'Set to 1 (lowest) through 9 (max) to change compression ' +
kkonganti@11:                 "level; lower compression is faster. Default: ${params.bbmerge_ziplevel}",
kkonganti@11:             cliflag: 'ziplevel=',
kkonganti@11:             clivalue: (params.bbmerge_ziplevel ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_ordered': [
kkonganti@11:             clihelp: 'Output reads in the same order as input. ' +
kkonganti@11:                 "Default: ${params.bbmerge_ordered}",
kkonganti@11:             cliflag: 'ordered=',
kkonganti@11:             clivalue: (params.bbmerge_ordered ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_qtrim': [
kkonganti@11:             clihelp: 'Trim read ends to remove bases with quality below --bbmerge_minq. ' +
kkonganti@11:                 'Trims BEFORE merging. Values: t (trim both ends), ' + 
kkonganti@11:                 'f (neither end), r (right end only), l (left end only). ' +
kkonganti@11:                 "Default: ${params.bbmerge_qtrim}",
kkonganti@11:             cliflag: 'qtrim=',
kkonganti@11:             clivalue: (params.bbmerge_qtrim ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_qtrim2': [
kkonganti@11:             clihelp: 'May be specified instead of --bbmerge_qtrim to perform trimming ' +
kkonganti@11:                 'only if merging is unsuccesful. then retry merging. ' +
kkonganti@11:                 "Default: ${params.bbmerge_qtrim2}",
kkonganti@11:             cliflag: 'qtrim2=',
kkonganti@11:             clivalue: (params.bbmerge_qtrim2 ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_trimq': [
kkonganti@11:             clihelp: 'Trim quality threshold. This may be comma-delimited list (ascending) ' +
kkonganti@11:                 "to try multiple values. Default: ${params.bbmerge_trimq}",
kkonganti@11:             cliflag: 'trimq=',
kkonganti@11:             clivalue: (params.bbmerge_trimq ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_minlength': [
kkonganti@11:             clihelp: '(ml) Reads shorter than this after trimming, but before ' +
kkonganti@11:                 'merging, will be discarded. Pairs will be discarded only' +
kkonganti@11:                 "if both are shorter. Default: ${params.bbmerge_minlength}",
kkonganti@11:             cliflag: 'minlength=',
kkonganti@11:             clivalue: (params.bbmerge_minlength ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_tbo': [
kkonganti@11:             clihelp: '(trimbyoverlap). Trim overlapping reads to remove right ' +
kkonganti@11:                 "most (3') non-overlaping portion instead of joining " +
kkonganti@11:                 "Default: ${params.bbmerge_tbo}",
kkonganti@11:             cliflag: 'tbo=',
kkonganti@11:             clivalue: (params.bbmerge_tbo ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_minavgquality': [
kkonganti@11:             clihelp: '(maq). Reads with average quality below this after trimming will ' +
kkonganti@11:                 "not be attempted to merge. Default: ${params.bbmerge_minavgquality}",
kkonganti@11:             cliflag: 'minavgquality=',
kkonganti@11:             clivalue: (params.bbmerge_minavgquality ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_trimpolya': [
kkonganti@11:             clihelp: 'Trim trailing poly-A tail from adapter output. Only affects ' +
kkonganti@11:                 'outadapter.  This also trims poly-A followed by poly-G, which ' +
kkonganti@11:                 "occurs on NextSeq. Default: ${params.bbmerge_trimpolya}",
kkonganti@11:             cliflag: 'trimpolya=',
kkonganti@11:             clivalue: (params.bbmerge_trimpolya ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_pfilter': [
kkonganti@11:             clihelp: 'Ban improbable overlaps. Higher is more strict. 0 will ' +
kkonganti@11:                 'disable the filter; 1 will allow only perfect overlaps. ' +
kkonganti@11:                 "Default: ${params.bbmerge_pfilter}",
kkonganti@11:             cliflag: 'pfilter=',
kkonganti@11:             clivalue: (params.bbmerge_pfilter ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_ouq': [
kkonganti@11:             clihelp: 'Calculate best overlap using quality values. ' +
kkonganti@11:                 "Default: ${params.bbmerge_ouq}",
kkonganti@11:             cliflag: 'ouq',
kkonganti@11:             clivalue: (params.bbmerge_ouq ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_owq': [
kkonganti@11:             clihelp: 'Calculate best overlap without using quality values. ' +
kkonganti@11:                 "Default: ${params.bbmerge_owq}",
kkonganti@11:             cliflag: 'owq=',
kkonganti@11:             clivalue: (params.bbmerge_owq ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_strict': [
kkonganti@11:             clihelp: 'Decrease false positive rate and merging rate. ' +
kkonganti@11:                 "Default: ${params.bbmerge_strict}",
kkonganti@11:             cliflag: 'strict=',
kkonganti@11:             clivalue: (params.bbmerge_strict ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_verystrict': [
kkonganti@11:             clihelp: 'Greatly decrease false positive rate and merging rate. ' +
kkonganti@11:                 "Default: ${params.bbmerge_verystrict}",
kkonganti@11:             cliflag: 'verystrict=',
kkonganti@11:             clivalue: (params.bbmerge_verystrict ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_ultrastrict': [
kkonganti@11:             clihelp: 'Decrease false positive rate and merging rate even more. ' +
kkonganti@11:                 "Default: ${params.bbmerge_ultrastrict}",
kkonganti@11:             cliflag: 'ultrastrict=',
kkonganti@11:             clivalue: (params.bbmerge_ultrastrict ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_maxstrict': [
kkonganti@11:             clihelp: 'Maxiamally decrease false positive rate and merging rate. ' +
kkonganti@11:                 "Default: ${params.bbmerge_maxstrict}",
kkonganti@11:             cliflag: 'maxstrict=',
kkonganti@11:             clivalue: (params.bbmerge_maxstrict ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_loose': [
kkonganti@11:             clihelp: 'Increase false positive rate and merging rate. ' +
kkonganti@11:                 "Default: ${params.bbmerge_loose}",
kkonganti@11:             cliflag: 'loose=',
kkonganti@11:             clivalue: (params.bbmerge_loose ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_veryloose': [
kkonganti@11:             clihelp: 'Greatly increase false positive rate and merging rate. ' +
kkonganti@11:                 "Default: ${params.bbmerge_veryloose}",
kkonganti@11:             cliflag: 'veryloose=',
kkonganti@11:             clivalue: (params.bbmerge_veryloose ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_ultraloose': [
kkonganti@11:             clihelp: 'Increase false positive rate and merging rate even more. ' +
kkonganti@11:                 "Default: ${params.bbmerge_ultraloose}",
kkonganti@11:             cliflag: 'ultraloose=',
kkonganti@11:             clivalue: (params.bbmerge_ultraloose ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_maxloose': [
kkonganti@11:             clihelp: 'Maximally increase false positive rate and merging rate. ' +
kkonganti@11:                 "Default: ${params.bbmerge_maxloose}",
kkonganti@11:             cliflag: 'maxloose=',
kkonganti@11:             clivalue: (params.bbmerge_maxloose ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_fast': [
kkonganti@11:             clihelp: 'Fastest possible preset. ' +
kkonganti@11:                 "Default: ${params.bbmerge_fast}",
kkonganti@11:             cliflag: 'fast=',
kkonganti@11:             clivalue: (params.bbmerge_fast ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_k': [
kkonganti@11:             clihelp: 'Kmer length.  31 (or less) is fastest and uses the least ' +
kkonganti@11:                 'memory, but higher values may be more accurate. ' +
kkonganti@11:                 '60 tends to work well for 150bp reads. ' +
kkonganti@11:                 "Default: ${params.bbmerge_k}",
kkonganti@11:             cliflag: 'k=',
kkonganti@11:             clivalue: (params.bbmerge_k ?: '')
kkonganti@11:         ],
kkonganti@11:         'bbmerge_prealloc': [
kkonganti@11:             clihelp: 'Pre-allocate memory rather than dynamically growing. ' +
kkonganti@11:                 'Faster and more memory-efficient for large datasets. ' +
kkonganti@11:                 'A float fraction (0-1) may be specified, default 1. ' +
kkonganti@11:                 "Default: ${params.bbmerge_prealloc}",
kkonganti@11:             cliflag: 'prealloc=',
kkonganti@11:             clivalue: (params.bbmerge_prealloc ?: '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }