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comparison 0.1.0/lib/help/salmonidx.nf @ 0:c8597e9e1a97

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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-1:000000000000 0:c8597e9e1a97
1 // Help text for salmon index within CPIPES.
2
3 def salmonidxHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'salmonidx_run': [
12 clihelp: 'Run `salmon index` tool. Default: ' +
13 (params.salmonidx_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'salmonidx_k': [
18 clihelp: 'The size of k-mers that should be used for the ' +
19 <<<<<<< HEAD
20 " quasi index. Defaut: ${params.salmonidx_k}",
21 =======
22 " quasi index. Default: ${params.salmonidx_k}",
23 >>>>>>> 0.5.0
24 cliflag: '-k',
25 clivalue: (params.salmonidx_k ?: '')
26 ],
27 'salmonidx_gencode': [
28 clihelp: 'This flag will expect the input transcript FASTA ' +
29 'to be in GENCODE format, and will split the transcript ' +
30 'name at the first `|` character. These reduced names ' +
31 'will be used in the output and when looking for these ' +
32 'transcripts in a gene to transcript GTF.' +
33 " Default: ${params.salmonidx_gencode}",
34 cliflag: '--gencode',
35 clivalue: (params.salmonidx_gencode ? ' ' : '')
36 ],
37 'salmonidx_features': [
38 clihelp: 'This flag will expect the input reference to be in the ' +
39 'tsv file format, and will split the feature name at the first ' +
40 '`tab` character. These reduced names will be used in the output ' +
41 'and when looking for the sequence of the features. GTF.' +
42 " Default: ${params.salmonidx_features}",
43 cliflag: '--features',
44 clivalue: (params.salmonidx_features ? ' ' : '')
45 ],
46 'salmonidx_keepDuplicates': [
47 clihelp: 'This flag will disable the default indexing behavior of ' +
48 'discarding sequence-identical duplicate transcripts. If this ' +
49 'flag is passed then duplicate transcripts that appear in the ' +
50 'input will be retained and quantified separately.' +
51 " Default: ${params.salmonidx_keepDuplicates}",
52 cliflag: '--keepDuplicates',
53 clivalue: (params.salmonidx_keepDuplicates ? ' ' : '')
54 ],
55 'salmonidx_keepFixedFasta': [
56 clihelp: 'Retain the fixed fasta file (without short ' +
57 'transcripts and duplicates, clipped, etc.) generated ' +
58 "during indexing. Default: ${params.salmonidx_keepFixedFasta}",
59 cliflag: '--keepFixedFasta',
60 clivalue: (params.salmonidx_keepFixedFasta ?: '')
61 ],
62 'salmonidx_filterSize': [
63 clihelp: 'The size of the Bloom filter that will be used ' +
64 'by TwoPaCo during indexing. The filter will be of ' +
65 'size 2^{filterSize}. A value of -1 means that the ' +
66 'filter size will be automatically set based on the ' +
67 'number of distinct k-mers in the input, as estimated by ' +
68 "nthll. Default: ${params.salmonidx_filterSize}",
69 cliflag: '--filterSize',
70 clivalue: (params.salmonidx_filterSize ?: '')
71 ],
72 'salmonidx_sparse': [
73 clihelp: 'Build the index using a sparse sampling of k-mer ' +
74 'positions This will require less memory (especially ' +
75 'during quantification), but will take longer to construct' +
76 'and can slow down mapping / alignment.' +
77 " Default: ${params.salmonidx_sparse}",
78 cliflag: '--sparse',
79 clivalue: (params.salmonidx_sparse ? ' ' : '')
80 ],
81 'salmonidx_n': [
82 clihelp: 'Do not clip poly-A tails from the ends of target ' +
83 "sequences. Default: ${params.salmonidx_n}",
84 cliflag: '-n',
85 clivalue: (params.salmonidx_n ? ' ' : '')
86 ]
87 ]
88
89 toolspecs.each {
90 k, v -> tool.text['--' + k] = "${v.clihelp}"
91 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
92 }
93
94 return tool
95 }