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comparison 0.4.2/lib/help/kraken2.nf @ 0:082e0091e813 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 // Help text for kraken2 within CPIPES.
2
3 def kraken2Help(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'kraken2_db': [
12 clihelp: "Absolute path to kraken database. Default: ${params.kraken2_db}",
13 cliflag: '--db',
14 clivalue: null
15 ],
16 'kraken2_confidence': [
17 clihelp: 'Confidence score threshold which must be ' +
18 "between 0 and 1. Default: ${params.kraken2_confidence}",
19 cliflag: '--confidence',
20 clivalue: (params.kraken2_confidence ?: '')
21 ],
22 'kraken2_quick': [
23 clihelp: "Quick operation (use first hit or hits). Default: ${params.kraken2_quick}",
24 cliflag: '--quick',
25 clivalue: (params.kraken2_quick ? ' ' : '')
26 ],
27 'kraken2_use_mpa_style': [
28 clihelp: "Report output like Kraken 1's " +
29 "kraken-mpa-report. Default: ${params.kraken2_use_mpa_style}",
30 cliflag: '--use-mpa-style',
31 clivalue: (params.kraken2_use_mpa_style ? ' ' : '')
32 ],
33 'kraken2_minimum_base_quality': [
34 clihelp: 'Minimum base quality used in classification ' +
35 " which is only effective with FASTQ input. Default: ${params.kraken2_minimum_base_quality}",
36 cliflag: '--minimum-base-quality',
37 clivalue: (params.kraken2_minimum_base_quality ?: '')
38 ],
39 'kraken2_report_zero_counts': [
40 clihelp: 'Report counts for ALL taxa, even if counts are zero. ' +
41 "Default: ${params.kraken2_report_zero_counts}",
42 cliflag: '--report-zero-counts',
43 clivalue: (params.kraken2_report_zero_counts ? ' ' : '')
44 ],
45 'kraken2_report_minmizer_data': [
46 clihelp: 'Report minimizer and distinct minimizer count' +
47 ' information in addition to normal Kraken report. ' +
48 "Default: ${params.kraken2_report_minimizer_data}",
49 cliflag: '--report-minimizer-data',
50 clivalue: (params.kraken2_report_minimizer_data ? ' ' : '')
51 ],
52 'kraken2_use_names': [
53 clihelp: 'Print scientific names instead of just taxids. ' +
54 "Default: ${params.kraken2_use_names}",
55 cliflag: '--use-names',
56 clivalue: (params.kraken2_use_names ? ' ' : '')
57 ],
58 'kraken2_extract_bug': [
59 clihelp: 'Extract the reads or contigs beloging to this bug. ' +
60 "Default: ${params.kraken2_extract_bug}",
61 cliflag: null,
62 clivalue: null
63 ]
64 ]
65
66 toolspecs.each {
67 k, v -> tool.text['--' + k] = "${v.clihelp}"
68 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
69 }
70
71 return tool
72 }