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comparison 0.6.1/lib/help/amrfinderplus.nf @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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10:1b9de878b04a 11:749faef1caa9
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 }