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comparison 0.5.0/lib/help/megahit.nf @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 // Help text for megahit within CPIPES.
2
3 def megahitHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'megahit_run': [
12 clihelp: 'Run MEGAHIT assembler. Default: ' +
13 (params.megahit_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'megahit_min_count': [
18 clihelp: '<int>. Minimum multiplicity for filtering (k_min+1)-mers. ' +
19 "Default: ${params.megahit_min_count}",
20 cliflag: '--min-count',
21 clivalue: (params.megahit_min_count ?: '')
22 ],
23 'megahit_k_list': [
24 clihelp: 'Comma-separated list of kmer size. All values must be odd, in ' +
25 "the range 15-255, increment should be <= 28. Ex: '21,29,39,59,79,99,119,141'. " +
26 "Default: ${params.megahit_k_list}",
27 cliflag: '--k-list',
28 clivalue: (params.megahit_k_list ?: '')
29 ],
30 'megahit_no_mercy': [
31 clihelp: 'Do not add mercy k-mers. ' +
32 "Default: ${params.megahit_no_mercy}",
33 cliflag: '--no-mercy',
34 clivalue: (params.megahit_no_mercy ? ' ' : '')
35 ],
36 'megahit_bubble_level': [
37 clihelp: '<int>. Intensity of bubble merging (0-2), 0 to disable. ' +
38 "Default: ${params.megahit_bubble_level}",
39 cliflag: '--bubble-level',
40 clivalue: (params.megahit_bubble_level ?: '')
41 ],
42 'megahit_merge_level': [
43 clihelp: '<l,s>. Merge complex bubbles of length <= l*kmer_size and ' +
44 "similarity >= s. Default: ${params.megahit_merge_level}",
45 cliflag: '--merge-level',
46 clivalue: (params.megahit_merge_level ?: '')
47 ],
48 'megahit_prune_level': [
49 clihelp: '<int>. Strength of low depth pruning (0-3). ' +
50 "Default: ${params.megahit_prune_level}",
51 cliflag: '--prune-level',
52 clivalue: (params.megahit_prune_level ?: '')
53 ],
54 'megahit_prune_depth': [
55 clihelp: '<int>. Remove unitigs with avg k-mer depth less than this value. ' +
56 "Default: ${params.megahit_prune_depth}",
57 cliflag: '--prune-depth',
58 clivalue: (params.megahit_prune_depth ?: '')
59 ],
60 'megahit_low_local_ratio': [
61 clihelp: '<float>. Ratio threshold to define low local coverage contigs. ' +
62 "Default: ${params.megahit_low_local_ratio}",
63 cliflag: '--low-local-ratio',
64 clivalue: (params.megahit_low_local_ratio ?: '')
65 ],
66 'megahit_max_tip_len': [
67 clihelp: '<int>. remove tips less than this value [<int> * k]. ' +
68 "Default: ${params.megahit_max_tip_len}",
69 cliflag: '--max-tip-len',
70 clivalue: (params.megahit_max_tip_len ?: '')
71 ],
72 'megahit_no_local': [
73 clihelp: 'Disable local assembly. ' +
74 "Default: ${params.megahit_no_local}",
75 cliflag: '--no-local',
76 clivalue: (params.megahit_no_local ? ' ' : '')
77 ],
78 'megahit_kmin_1pass': [
79 clihelp: 'Use 1pass mode to build SdBG of k_min. ' +
80 "Default: ${params.megahit_kmin_1pass}",
81 cliflag: '--kmin-1pass',
82 clivalue: (params.megahit_kmin_1pass ? ' ' : '')
83 ],
84 'megahit_preset': [
85 clihelp: '<str>. Override a group of parameters. Valid values are '+
86 "meta-sensitive which enforces '--min-count 1 --k-list 21,29,39,49,...,129,141', " +
87 'meta-large (large & complex metagenomes, like soil) which enforces ' +
88 "'--k-min 27 --k-max 127 --k-step 10'. " +
89 "Default: ${params.megahit_preset}",
90 cliflag: '--preset',
91 clivalue: (params.megahit_preset ?: '')
92 ],
93 'megahit_mem_flag': [
94 clihelp: '<int>. SdBG builder memory mode. 0: minimum; 1: moderate; 2: use all memory specified. ' +
95 "Default: ${params.megahit_mem_flag}",
96 cliflag: '--mem-flag',
97 clivalue: (params.megahit_mem_flag ?: '')
98 ],
99 'megahit_min_contig_len': [
100 clihelp: '<int>. Minimum length of contigs to output. ' +
101 "Default: ${params.megahit_min_contig_len}",
102 cliflag: '--use-gpu',
103 clivalue: (params.megahit_min_contig_len ?: '')
104 ]
105 ]
106
107 toolspecs.each {
108 k, v -> tool.text['--' + k] = "${v.clihelp}"
109 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
110 }
111
112 return tool
113 }