Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.0/lib/help/megahit.nf @ 102:4425d68a184c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:54:24 -0400
parents ce6d9548fe89
children
rev   line source
kkonganti@101 1 // Help text for megahit within CPIPES.
kkonganti@101 2
kkonganti@101 3 def megahitHelp(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 'megahit_run': [
kkonganti@101 12 clihelp: 'Run MEGAHIT assembler. Default: ' +
kkonganti@101 13 (params.megahit_run ?: false),
kkonganti@101 14 cliflag: null,
kkonganti@101 15 clivalue: null
kkonganti@101 16 ],
kkonganti@101 17 'megahit_min_count': [
kkonganti@101 18 clihelp: '<int>. Minimum multiplicity for filtering (k_min+1)-mers. ' +
kkonganti@101 19 "Defaut: ${params.megahit_min_count}",
kkonganti@101 20 cliflag: '--min-count',
kkonganti@101 21 clivalue: (params.megahit_min_count ?: '')
kkonganti@101 22 ],
kkonganti@101 23 'megahit_k_list': [
kkonganti@101 24 clihelp: 'Comma-separated list of kmer size. All values must be odd, in ' +
kkonganti@101 25 "the range 15-255, increment should be <= 28. Ex: '21,29,39,59,79,99,119,141'. " +
kkonganti@101 26 "Default: ${params.megahit_k_list}",
kkonganti@101 27 cliflag: '--k-list',
kkonganti@101 28 clivalue: (params.megahit_k_list ?: '')
kkonganti@101 29 ],
kkonganti@101 30 'megahit_no_mercy': [
kkonganti@101 31 clihelp: 'Do not add mercy k-mers. ' +
kkonganti@101 32 "Default: ${params.megahit_no_mercy}",
kkonganti@101 33 cliflag: '--no-mercy',
kkonganti@101 34 clivalue: (params.megahit_no_mercy ? ' ' : '')
kkonganti@101 35 ],
kkonganti@101 36 'megahit_bubble_level': [
kkonganti@101 37 clihelp: '<int>. Intensity of bubble merging (0-2), 0 to disable. ' +
kkonganti@101 38 "Default: ${params.megahit_bubble_level}",
kkonganti@101 39 cliflag: '--bubble-level',
kkonganti@101 40 clivalue: (params.megahit_bubble_level ?: '')
kkonganti@101 41 ],
kkonganti@101 42 'megahit_merge_level': [
kkonganti@101 43 clihelp: '<l,s>. Merge complex bubbles of length <= l*kmer_size and ' +
kkonganti@101 44 "similarity >= s. Default: ${params.megahit_merge_level}",
kkonganti@101 45 cliflag: '--merge-level',
kkonganti@101 46 clivalue: (params.megahit_merge_level ?: '')
kkonganti@101 47 ],
kkonganti@101 48 'megahit_prune_level': [
kkonganti@101 49 clihelp: '<int>. Strength of low depth pruning (0-3). ' +
kkonganti@101 50 "Default: ${params.megahit_prune_level}",
kkonganti@101 51 cliflag: '--prune-level',
kkonganti@101 52 clivalue: (params.megahit_prune_level ?: '')
kkonganti@101 53 ],
kkonganti@101 54 'megahit_prune_depth': [
kkonganti@101 55 clihelp: '<int>. Remove unitigs with avg k-mer depth less than this value. ' +
kkonganti@101 56 "Default: ${params.megahit_prune_depth}",
kkonganti@101 57 cliflag: '--prune-depth',
kkonganti@101 58 clivalue: (params.megahit_prune_depth ?: '')
kkonganti@101 59 ],
kkonganti@101 60 'megahit_low_local_ratio': [
kkonganti@101 61 clihelp: '<float>. Ratio threshold to define low local coverage contigs. ' +
kkonganti@101 62 "Default: ${params.megahit_low_local_ratio}",
kkonganti@101 63 cliflag: '--low-local-ratio',
kkonganti@101 64 clivalue: (params.megahit_low_local_ratio ?: '')
kkonganti@101 65 ],
kkonganti@101 66 'megahit_max_tip_len': [
kkonganti@101 67 clihelp: '<int>. remove tips less than this value [<int> * k]. ' +
kkonganti@101 68 "Default: ${params.megahit_max_tip_len}",
kkonganti@101 69 cliflag: '--max-tip-len',
kkonganti@101 70 clivalue: (params.megahit_max_tip_len ?: '')
kkonganti@101 71 ],
kkonganti@101 72 'megahit_no_local': [
kkonganti@101 73 clihelp: 'Disable local assembly. ' +
kkonganti@101 74 "Default: ${params.megahit_no_local}",
kkonganti@101 75 cliflag: '--no-local',
kkonganti@101 76 clivalue: (params.megahit_no_local ? ' ' : '')
kkonganti@101 77 ],
kkonganti@101 78 'megahit_kmin_1pass': [
kkonganti@101 79 clihelp: 'Use 1pass mode to build SdBG of k_min. ' +
kkonganti@101 80 "Default: ${params.megahit_kmin_1pass}",
kkonganti@101 81 cliflag: '--kmin-1pass',
kkonganti@101 82 clivalue: (params.megahit_kmin_1pass ? ' ' : '')
kkonganti@101 83 ],
kkonganti@101 84 'megahit_preset': [
kkonganti@101 85 clihelp: '<str>. Override a group of parameters. Valid values are '+
kkonganti@101 86 "meta-sensitive which enforces '--min-count 1 --k-list 21,29,39,49,...,129,141', " +
kkonganti@101 87 'meta-large (large & complex metagenomes, like soil) which enforces ' +
kkonganti@101 88 "'--k-min 27 --k-max 127 --k-step 10'. " +
kkonganti@101 89 "Default: ${params.megahit_preset}",
kkonganti@101 90 cliflag: '--preset',
kkonganti@101 91 clivalue: (params.megahit_preset ?: '')
kkonganti@101 92 ],
kkonganti@101 93 'megahit_mem_flag': [
kkonganti@101 94 clihelp: '<int>. SdBG builder memory mode. 0: minimum; 1: moderate; 2: use all memory specified. ' +
kkonganti@101 95 "Default: ${params.megahit_mem_flag}",
kkonganti@101 96 cliflag: '--mem-flag',
kkonganti@101 97 clivalue: (params.megahit_mem_flag ?: '')
kkonganti@101 98 ],
kkonganti@101 99 'megahit_min_contig_len': [
kkonganti@101 100 clihelp: '<int>. Minimum length of contigs to output. ' +
kkonganti@101 101 "Default: ${params.megahit_min_contig_len}",
kkonganti@101 102 cliflag: '--use-gpu',
kkonganti@101 103 clivalue: (params.megahit_min_contig_len ?: '')
kkonganti@101 104 ]
kkonganti@101 105 ]
kkonganti@101 106
kkonganti@101 107 toolspecs.each {
kkonganti@101 108 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@101 109 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@101 110 }
kkonganti@101 111
kkonganti@101 112 return tool
kkonganti@101 113 }