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annotate 0.4.0/lib/help/amrfinderplus.nf @ 102:4425d68a184c

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:54:24 -0400
parents ce6d9548fe89
children
rev   line source
kkonganti@101 1 def amrfinderplusHelp(params) {
kkonganti@101 2
kkonganti@101 3 Map tool = [:]
kkonganti@101 4 Map toolspecs = [:]
kkonganti@101 5 tool.text = [:]
kkonganti@101 6 tool.helpparams = [:]
kkonganti@101 7
kkonganti@101 8 toolspecs = [
kkonganti@101 9 'amrfinderplus_run': [
kkonganti@101 10 clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}",
kkonganti@101 11 cliflag: null,
kkonganti@101 12 clivalue: null
kkonganti@101 13 ],
kkonganti@101 14 'amrfinderplus_db': [
kkonganti@101 15 clihelp: 'Path to AMRFinderPlus database. Please note that ' +
kkonganti@101 16 ' the databases should be ready and formatted with blast for use. ' +
kkonganti@101 17 'Please read more at: ' +
kkonganti@101 18 'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' +
kkonganti@101 19 "Default: ${params.amrfinderplus_db}",
kkonganti@101 20 cliflag: '--database',
kkonganti@101 21 clivalue: (params.amrfinderplus_db ?: '')
kkonganti@101 22 ],
kkonganti@101 23 'amrfinderplus_genes': [
kkonganti@101 24 clihelp: 'Add the plus genes to the report',
kkonganti@101 25 cliflag: '--plus',
kkonganti@101 26 clivalue: (params.amrfinderplus_genes ? ' ' : '')
kkonganti@101 27 ]
kkonganti@101 28 ]
kkonganti@101 29
kkonganti@101 30 toolspecs.each {
kkonganti@101 31 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@101 32 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@101 33 }
kkonganti@101 34
kkonganti@101 35 return tool
kkonganti@101 36 }