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comparison 0.5.0/lib/help/mashsketch.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 mash sketch within CPIPES.
2
3 def mashsketchHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'mashsketch_run': [
12 clihelp: 'Run `mash screen` tool. Default: ' +
13 (params.mashsketch_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'mashsketch_l': [
18 clihelp: 'List input. Lines in each <input> specify paths to sequence files, ' +
19 'one per line. ' +
20 "Default: ${params.mashsketch_l}",
21 cliflag: '-l',
22 clivalue: (params.mashsketch_l ? ' ' : '')
23 ],
24 'mashsketch_I': [
25 clihelp: '<path> ID field for sketch of reads (instead of first sequence ID). ' +
26 "Default: ${params.mashsketch_I}",
27 cliflag: '-I',
28 clivalue: (params.mashsketch_I ?: '')
29 ],
30 'mashsketch_C': [
31 clihelp: '<path> Comment for a sketch of reads (instead of first sequence comment). ' +
32 "Default: ${params.mashsketch_C}",
33 cliflag: '-C',
34 clivalue: (params.mashsketch_C ?: '')
35 ],
36 'mashsketch_k': [
37 clihelp: '<int> K-mer size. Hashes will be based on strings of this many ' +
38 'nucleotides. Canonical nucleotides are used by default (see ' +
39 'Alphabet options below). (1-32) ' +
40 "Default: ${params.mashsketch_k}",
41 cliflag: '-k',
42 clivalue: (params.mashsketch_k ?: '')
43 ],
44 'mashsketch_s': [
45 clihelp: '<int> Sketch size. Each sketch will have at most this many non-redundant ' +
46 'min-hashes. ' +
47 "Default: ${params.mashsketch_s}",
48 cliflag: '-s',
49 clivalue: (params.mashsketch_s ?: '')
50 ],
51 'mashsketch_i': [
52 clihelp: 'Sketch individual sequences, rather than whole files, e.g. for ' +
53 'multi-fastas of single-chromosome genomes or pair-wise gene ' +
54 'comparisons. ' +
55 "Default: ${params.mashsketch_i}",
56 cliflag: '-i',
57 clivalue: (params.mashsketch_i ? ' ' : '')
58 ],
59 'mashsketch_S': [
60 clihelp: '<int> Seed to provide to the hash function. (0-4294967296) [42] ' +
61 "Default: ${params.mashsketch_S}",
62 cliflag: '-S',
63 clivalue: (params.mashsketch_S ?: '')
64 ],
65
66 'mashsketch_w': [
67 clihelp: '<num> Probability threshold for warning about low k-mer size. (0-1) ' +
68 "Default: ${params.mashsketch_w}",
69 cliflag: '-w',
70 clivalue: (params.mashsketch_w ?: '')
71 ],
72 'mashsketch_r': [
73 clihelp: 'Input is a read set. See Reads options below. Incompatible with ' +
74 '--mashsketch_i. ' +
75 "Default: ${params.mashsketch_r}",
76 cliflag: '-r',
77 clivalue: (params.mashsketch_r ? ' ' : '')
78 ],
79 'mashsketch_b': [
80 clihelp: '<size> Use a Bloom filter of this size (raw bytes or with K/M/G/T) to ' +
81 'filter out unique k-mers. This is useful if exact filtering with ' +
82 '--mashsketch_m uses too much memory. However, some unique k-mers may pass ' +
83 'erroneously, and copies cannot be counted beyond 2. Implies --mashsketch_r. ' +
84 "Default: ${params.mashsketch_b}",
85 cliflag: '-b',
86 clivalue: (params.mashsketch_b ?: '')
87 ],
88 'mashsketch_m': [
89 clihelp: '<int> Minimum copies of each k-mer required to pass noise filter for ' +
90 'reads. Implies --mashsketch_r. ' +
91 "Default: ${params.mashsketch_r}",
92 cliflag: '-m',
93 clivalue: (params.mashsketch_m ?: '')
94 ],
95 'mashsketch_c': [
96 clihelp: '<num> Target coverage. Sketching will conclude if this coverage is ' +
97 'reached before the end of the input file (estimated by average ' +
98 'k-mer multiplicity). Implies --mashsketch_r. ' +
99 "Default: ${params.mashsketch_c}",
100 cliflag: '-c',
101 clivalue: (params.mashsketch_c ?: '')
102 ],
103 'mashsketch_g': [
104 clihelp: '<size> Genome size (raw bases or with K/M/G/T). If specified, will be used ' +
105 'for p-value calculation instead of an estimated size from k-mer ' +
106 'content. Implies --mashsketch_r. ' +
107 "Default: ${params.mashsketch_g}",
108 cliflag: '-g',
109 clivalue: (params.mashsketch_g ?: '')
110 ],
111 'mashsketch_n': [
112 clihelp: 'Preserve strand (by default, strand is ignored by using canonical ' +
113 'DNA k-mers, which are alphabetical minima of forward-reverse ' +
114 'pairs). Implied if an alphabet is specified with --mashsketch_a ' +
115 'or --mashsketch_z. ' +
116 "Default: ${params.mashsketch_n}",
117 cliflag: '-n',
118 clivalue: (params.mashsketch_n ? ' ' : '')
119 ],
120 'mashsketch_a': [
121 clihelp: 'Use amino acid alphabet (A-Z, except BJOUXZ). Implies ' +
122 '--mashsketch_n --mashsketch_k 9. ' +
123 "Default: ${params.mashsketch_a}",
124 cliflag: '-a',
125 clivalue: (params.mashsketch_a ? ' ' : '')
126 ],
127 'mashsketch_z': [
128 clihelp: '<text> Alphabet to base hashes on (case ignored by default; ' +
129 'see --mashsketch_Z). K-mers with other characters will be ' +
130 'ignored. Implies --mashsketch_n. ' +
131 "Default: ${params.mashsketch_z}",
132 cliflag: '-z',
133 clivalue: (params.mashsketch_z ?: '')
134 ],
135 'mashsketch_Z': [
136 clihelp: 'Preserve case in k-mers and alphabet (case is ignored by default). ' +
137 'Sequence letters whose case is not in the current alphabet will be ' +
138 'skipped when sketching. ' +
139 "Default: ${params.mashsketch_Z}",
140 cliflag: '-Z',
141 clivalue: (params.mashsketch_Z ?: '')
142 ]
143 ]
144
145 toolspecs.each {
146 k, v -> tool.text['--' + k] = "${v.clihelp}"
147 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
148 }
149
150 return tool
151 }