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comparison 0.7.0/lib/help/mashscreen.nf @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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16:b90e5a7a3d4f 17:0e7a0053e4a6
1 // Help text for mash screen within CPIPES.
2
3 def mashscreenHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'mashscreen_run': [
12 clihelp: 'Run `mash screen` tool. Default: ' +
13 (params.mashscreen_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'mashscreen_w': [
18 clihelp: 'Winner-takes-all strategy for identity estimates. After counting ' +
19 'hashes for each query, hashes that appear in multiple queries will ' +
20 'be removed from all except the one with the best identity (ties ' +
21 'broken by larger query), and other identities will be reduced. This ' +
22 'removes output redundancy, providing a rough compositional outline. ' +
23 " Default: ${params.mashscreen_w}",
24 cliflag: '-w',
25 clivalue: (params.mashscreen_w ? ' ' : '')
26 ],
27 'mashscreen_i': [
28 clihelp: 'Minimum identity to report. Inclusive unless set to zero, in which ' +
29 'case only identities greater than zero (i.e. with at least one ' +
30 'shared hash) will be reported. Set to -1 to output everything. ' +
31 "(-1-1). Default: ${params.mashscreen_i}",
32 cliflag: '-i',
33 clivalue: (params.mashscreen_i ?: '')
34 ],
35 'mashscreen_v': [
36 clihelp: 'Maximum p-value to report (0-1). ' +
37 "Default: ${params.mashscreen_v}",
38 cliflag: '-v',
39 clivalue: (params.mashscreen_v ?: '')
40 ]
41 ]
42
43 toolspecs.each {
44 k, v -> tool.text['--' + k] = "${v.clihelp}"
45 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
46 }
47
48 return tool
49 }