|
0
|
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 } |
