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comparison 0.7.0/lib/help/amrfinderplus.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 def amrfinderplusHelp(params) {
2
3 Map tool = [:]
4 Map toolspecs = [:]
5 tool.text = [:]
6 tool.helpparams = [:]
7
8 toolspecs = [
9 'amrfinderplus_run': [
10 clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}",
11 cliflag: null,
12 clivalue: null
13 ],
14 'amrfinderplus_db': [
15 clihelp: 'Path to AMRFinderPlus database. Please note that ' +
16 ' the databases should be ready and formatted with blast for use. ' +
17 'Please read more at: ' +
18 'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' +
19 "Default: ${params.amrfinderplus_db}",
20 cliflag: '--database',
21 clivalue: (params.amrfinderplus_db ?: '')
22 ],
23 'amrfinderplus_genes': [
24 clihelp: 'Add the plus genes to the report',
25 cliflag: '--plus',
26 clivalue: (params.amrfinderplus_genes ? ' ' : '')
27 ]
28 ]
29
30 toolspecs.each {
31 k, v -> tool.text['--' + k] = "${v.clihelp}"
32 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
33 }
34
35 return tool
36 }