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comparison 1.0.0/lib/help/medakastitch.nf @ 0:801b85b03a17 draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 // Help text for medaka `stitch` within CPIPES.
2
3 def medakastitchHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'medakastitch_min_depth': [
12 clihelp: 'Sites with depth lower than this will not be polished. ' +
13 "Default: ${params.medakastitch_min_depth}",
14 cliflag: '--min_depth',
15 clivalue: (params.medakastitch_min_depth ?: '')
16 ],
17 'medakastitch_no_fillgaps': [
18 clihelp: "Don't fill gaps in consensus sequence with draft sequence. " +
19 "Default: ${params.medakastitch_no_fillgaps}",
20 cliflag: '--no-fillgaps',
21 clivalue: (params.medakastitch_no_fillgaps ? ' ' : '')
22 ],
23 'medakastitch_fill_char': [
24 clihelp: 'Use a designated character to fill gaps. ' +
25 "Default: ${params.medakastitch_fill_char}",
26 cliflag: '--fill_char',
27 clivalue: (params.medakastitch_fill_char ?: '')
28 ],
29 'medakastitch_regions': [
30 clihelp: 'Genomic regions to analyze, or a bed file. ' +
31 "Default: ${params.medakastitch_regions}",
32 cliflag: '--regions',
33 clivalue: (params.medakastitch_regions ?: '')
34 ],
35 'medakastitch_quals': [
36 clihelp: 'Output with per-base quality scores (fastq). ' +
37 "Default: ${params.medakastitch_quals}",
38 cliflag: '--qualities',
39 clivalue: (params.medakastitch_quals ? ' ' : '')
40 ]
41 ]
42
43 toolspecs.each {
44 k, v -> tool.text['--' + k] = "${v.clihelp}"
45 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
46 }
47
48 return tool
49 }