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comparison 0.5.0/lib/help/kronaktimporttext.nf @ 0:97cd2f532efe

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author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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-1:000000000000 0:97cd2f532efe
1 // Help text for ktImportText (krona) within CPIPES.
2
3 def kronaktimporttextHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'krona_ktIT_run': [
12 clihelp: 'Run the ktImportText (ktIT) from krona. Default: ' +
13 (params.krona_ktIT_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'krona_ktIT_n': [
18 clihelp: 'Name of the highest level. ' +
19 "Default: ${params.krona_ktIT_n}",
20 cliflag: '-n',
21 clivalue: (params.krona_ktIT_n ?: '')
22 ],
23 'krona_ktIT_q': [
24 clihelp: 'Input file(s) do not have a field for quantity. ' +
25 "Default: ${params.krona_ktIT_q}",
26 cliflag: '-q',
27 clivalue: (params.krona_ktIT_q ? ' ' : '')
28 ],
29 'krona_ktIT_c': [
30 clihelp: 'Combine data from each file, rather than creating separate datasets '
31 + 'within the chart. ' +
32 "Default: ${params.krona_ktIT_c}",
33 cliflag: '-c',
34 clivalue: (params.krona_ktIT_c ? ' ' : '')
35 ]
36 ]
37
38 toolspecs.each {
39 k, v -> tool.text['--' + k] = "${v.clihelp}"
40 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
41 }
42
43 return tool
44 }