Mercurial > repos > kkonganti > cfsan_cronology

annotate 0.1.0/lib/help/megahit.nf @ 0:c8597e9e1a97

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
parents
children
rev   line source
kkonganti@0 1 // Help text for megahit within CPIPES.
kkonganti@0 2
kkonganti@0 3 def megahitHelp(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 'megahit_run': [
kkonganti@0 12 clihelp: 'Run MEGAHIT assembler. Default: ' +
kkonganti@0 13 (params.megahit_run ?: false),
kkonganti@0 14 cliflag: null,
kkonganti@0 15 clivalue: null
kkonganti@0 16 ],
kkonganti@0 17 'megahit_min_count': [
kkonganti@0 18 clihelp: '<int>. Minimum multiplicity for filtering (k_min+1)-mers. ' +
kkonganti@0 19 "Default: ${params.megahit_min_count}",
kkonganti@0 20 cliflag: '--min-count',
kkonganti@0 21 clivalue: (params.megahit_min_count ?: '')
kkonganti@0 22 ],
kkonganti@0 23 'megahit_k_list': [
kkonganti@0 24 clihelp: 'Comma-separated list of kmer size. All values must be odd, in ' +
kkonganti@0 25 "the range 15-255, increment should be <= 28. Ex: '21,29,39,59,79,99,119,141'. " +
kkonganti@0 26 "Default: ${params.megahit_k_list}",
kkonganti@0 27 cliflag: '--k-list',
kkonganti@0 28 clivalue: (params.megahit_k_list ?: '')
kkonganti@0 29 ],
kkonganti@0 30 'megahit_no_mercy': [
kkonganti@0 31 clihelp: 'Do not add mercy k-mers. ' +
kkonganti@0 32 "Default: ${params.megahit_no_mercy}",
kkonganti@0 33 cliflag: '--no-mercy',
kkonganti@0 34 clivalue: (params.megahit_no_mercy ? ' ' : '')
kkonganti@0 35 ],
kkonganti@0 36 'megahit_bubble_level': [
kkonganti@0 37 clihelp: '<int>. Intensity of bubble merging (0-2), 0 to disable. ' +
kkonganti@0 38 "Default: ${params.megahit_bubble_level}",
kkonganti@0 39 cliflag: '--bubble-level',
kkonganti@0 40 clivalue: (params.megahit_bubble_level ?: '')
kkonganti@0 41 ],
kkonganti@0 42 'megahit_merge_level': [
kkonganti@0 43 clihelp: '<l,s>. Merge complex bubbles of length <= l*kmer_size and ' +
kkonganti@0 44 "similarity >= s. Default: ${params.megahit_merge_level}",
kkonganti@0 45 cliflag: '--merge-level',
kkonganti@0 46 clivalue: (params.megahit_merge_level ?: '')
kkonganti@0 47 ],
kkonganti@0 48 'megahit_prune_level': [
kkonganti@0 49 clihelp: '<int>. Strength of low depth pruning (0-3). ' +
kkonganti@0 50 "Default: ${params.megahit_prune_level}",
kkonganti@0 51 cliflag: '--prune-level',
kkonganti@0 52 clivalue: (params.megahit_prune_level ?: '')
kkonganti@0 53 ],
kkonganti@0 54 'megahit_prune_depth': [
kkonganti@0 55 clihelp: '<int>. Remove unitigs with avg k-mer depth less than this value. ' +
kkonganti@0 56 "Default: ${params.megahit_prune_depth}",
kkonganti@0 57 cliflag: '--prune-depth',
kkonganti@0 58 clivalue: (params.megahit_prune_depth ?: '')
kkonganti@0 59 ],
kkonganti@0 60 'megahit_low_local_ratio': [
kkonganti@0 61 clihelp: '<float>. Ratio threshold to define low local coverage contigs. ' +
kkonganti@0 62 "Default: ${params.megahit_low_local_ratio}",
kkonganti@0 63 cliflag: '--low-local-ratio',
kkonganti@0 64 clivalue: (params.megahit_low_local_ratio ?: '')
kkonganti@0 65 ],
kkonganti@0 66 'megahit_max_tip_len': [
kkonganti@0 67 clihelp: '<int>. remove tips less than this value [<int> * k]. ' +
kkonganti@0 68 "Default: ${params.megahit_max_tip_len}",
kkonganti@0 69 cliflag: '--max-tip-len',
kkonganti@0 70 clivalue: (params.megahit_max_tip_len ?: '')
kkonganti@0 71 ],
kkonganti@0 72 'megahit_no_local': [
kkonganti@0 73 clihelp: 'Disable local assembly. ' +
kkonganti@0 74 "Default: ${params.megahit_no_local}",
kkonganti@0 75 cliflag: '--no-local',
kkonganti@0 76 clivalue: (params.megahit_no_local ? ' ' : '')
kkonganti@0 77 ],
kkonganti@0 78 'megahit_kmin_1pass': [
kkonganti@0 79 clihelp: 'Use 1pass mode to build SdBG of k_min. ' +
kkonganti@0 80 "Default: ${params.megahit_kmin_1pass}",
kkonganti@0 81 cliflag: '--kmin-1pass',
kkonganti@0 82 clivalue: (params.megahit_kmin_1pass ? ' ' : '')
kkonganti@0 83 ],
kkonganti@0 84 'megahit_preset': [
kkonganti@0 85 clihelp: '<str>. Override a group of parameters. Valid values are '+
kkonganti@0 86 "meta-sensitive which enforces '--min-count 1 --k-list 21,29,39,49,...,129,141', " +
kkonganti@0 87 'meta-large (large & complex metagenomes, like soil) which enforces ' +
kkonganti@0 88 "'--k-min 27 --k-max 127 --k-step 10'. " +
kkonganti@0 89 "Default: ${params.megahit_preset}",
kkonganti@0 90 cliflag: '--preset',
kkonganti@0 91 clivalue: (params.megahit_preset ?: '')
kkonganti@0 92 ],
kkonganti@0 93 'megahit_mem_flag': [
kkonganti@0 94 clihelp: '<int>. SdBG builder memory mode. 0: minimum; 1: moderate; 2: use all memory specified. ' +
kkonganti@0 95 "Default: ${params.megahit_mem_flag}",
kkonganti@0 96 cliflag: '--mem-flag',
kkonganti@0 97 clivalue: (params.megahit_mem_flag ?: '')
kkonganti@0 98 ],
kkonganti@0 99 'megahit_min_contig_len': [
kkonganti@0 100 clihelp: '<int>. Minimum length of contigs to output. ' +
kkonganti@0 101 "Default: ${params.megahit_min_contig_len}",
kkonganti@0 102 cliflag: '--use-gpu',
kkonganti@0 103 clivalue: (params.megahit_min_contig_len ?: '')
kkonganti@0 104 ]
kkonganti@0 105 ]
kkonganti@0 106
kkonganti@0 107 toolspecs.each {
kkonganti@0 108 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0 109 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0 110 }
kkonganti@0 111
kkonganti@0 112 return tool
kkonganti@0 113 }