Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/lib/help/abricate.nf @ 0:9e8b1c747a6a draft default tip

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author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 // Help text for abricate within CPIPES.
2
3 def abricateHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'abricate_run': [
12 clihelp: 'Run ABRicate tool. Default: ' +
13 (params.abricate_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'abricate_minid': [
18 clihelp: 'Minimum DNA %identity. ' +
19 "Default: " + (params.abricate_minid ?: 80),
20 cliflag: '--minid',
21 clivalue: (params.abricate_minid ?: 80)
22 ],
23 'abricate_mincov': [
24 clihelp: 'Minimum DNA %coverage. ' +
25 "Default: " + (params.abricate_mincov ?: 80),
26 cliflag: '--mincov',
27 clivalue: (params.abricate_mincov ?: 80)
28 ],
29 'abricate_datadir': [
30 clihelp: 'ABRicate databases folder. ' +
31 "Default: " + (params.abricate_datadir ?: 'undefined'),
32 cliflag: '--datadir',
33 clivalue: (params.abricate_datadir ?: '')
34 ]
35 ]
36
37 toolspecs.each {
38 k, v -> tool.text['--' + k] = "${v.clihelp}"
39 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
40 }
41
42 return tool
43 }