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comparison 0.5.0/lib/help/sourmashsketch.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 sourmash sketch dna within CPIPES.
2
3 def sourmashsketchHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'sourmashsketch_run': [
12 clihelp: 'Run `sourmash sketch dna` tool. Default: ' +
13 (params.sourmashsketch_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'sourmashsketch_mode': [
18 clihelp: "Select which type of signatures to be created: dna, protein, fromfile or translate. "
19 + "Default: ${params.sourmashsketch_mode}",
20 cliflag: "${params.sourmashsketch_mode}",
21 clivalue: ' '
22 ],
23 'sourmashsketch_p': [
24 clihelp: 'Signature parameters to use. ' +
25 "Default: ${params.sourmashsketch_p}",
26 cliflag: '-p',
27 clivalue: (params.sourmashsketch_p ?: '')
28 ],
29 'sourmashsketch_file': [
30 clihelp: '<path> A text file containing a list of sequence files to load. ' +
31 "Default: ${params.sourmashsketch_file}",
32 cliflag: '--from-file',
33 clivalue: (params.sourmashsketch_file ?: '')
34 ],
35 'sourmashsketch_f': [
36 clihelp: 'Recompute signatures even if the file exists. ' +
37 "Default: ${params.sourmashsketch_f}",
38 cliflag: '-f',
39 clivalue: (params.sourmashsketch_f ? ' ' : '')
40 ],
41 'sourmashsketch_merge': [
42 clihelp: 'Merge all input files into one signature file with the specified name. ' +
43 "Default: ${params.sourmashsketch_merge}",
44 cliflag: '--merge',
45 clivalue: (params.sourmashsketch_merge ? ' ' : '')
46 ],
47 'sourmashsketch_singleton': [
48 clihelp: 'Compute a signature for each sequence record individually. ' +
49 "Default: ${params.sourmashsketch_singleton}",
50 cliflag: '--singleton',
51 clivalue: (params.sourmashsketch_singleton ? ' ' : '')
52 ],
53 'sourmashsketch_name': [
54 clihelp: 'Name the signature generated from each file after the first record in the file. ' +
55 "Default: ${params.sourmashsketch_name}",
56 cliflag: '--name-from-first',
57 clivalue: (params.sourmashsketch_name ? ' ' : '')
58 ],
59 'sourmashsketch_randomize': [
60 clihelp: 'Shuffle the list of input files randomly. ' +
61 "Default: ${params.sourmashsketch_randomize}",
62 cliflag: '--randomize',
63 clivalue: (params.sourmashsketch_randomize ? ' ' : '')
64 ]
65 ]
66
67 toolspecs.each {
68 k, v -> tool.text['--' + k] = "${v.clihelp}"
69 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
70 }
71
72 return tool
73 }