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