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annotate 0.3.0/lib/help/amrfinderplus.nf @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
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kkonganti@92 1 def amrfinderplusHelp(params) {
kkonganti@92 2
kkonganti@92 3 Map tool = [:]
kkonganti@92 4 Map toolspecs = [:]
kkonganti@92 5 tool.text = [:]
kkonganti@92 6 tool.helpparams = [:]
kkonganti@92 7
kkonganti@92 8 toolspecs = [
kkonganti@92 9 'amrfinderplus_run': [
kkonganti@92 10 clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}",
kkonganti@92 11 cliflag: null,
kkonganti@92 12 clivalue: null
kkonganti@92 13 ],
kkonganti@92 14 'amrfinderplus_db': [
kkonganti@92 15 clihelp: 'Path to AMRFinderPlus database. Please note that ' +
kkonganti@92 16 ' the databases should be ready and formatted with blast for use. ' +
kkonganti@92 17 'Please read more at: ' +
kkonganti@92 18 'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' +
kkonganti@92 19 "Default: ${params.amrfinderplus_db}",
kkonganti@92 20 cliflag: '--database',
kkonganti@92 21 clivalue: (params.amrfinderplus_db ?: '')
kkonganti@92 22 ],
kkonganti@92 23 'amrfinderplus_genes': [
kkonganti@92 24 clihelp: 'Add the plus genes to the report',
kkonganti@92 25 cliflag: '--plus',
kkonganti@92 26 clivalue: (params.amrfinderplus_genes ? ' ' : '')
kkonganti@92 27 ]
kkonganti@92 28 ]
kkonganti@92 29
kkonganti@92 30 toolspecs.each {
kkonganti@92 31 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@92 32 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@92 33 }
kkonganti@92 34
kkonganti@92 35 return tool
kkonganti@92 36 }