kkonganti@101: def amrfinderplusHelp(params) {
kkonganti@101: 
kkonganti@101:     Map tool = [:]
kkonganti@101:     Map toolspecs = [:]
kkonganti@101:     tool.text = [:]
kkonganti@101:     tool.helpparams = [:]
kkonganti@101: 
kkonganti@101:     toolspecs = [
kkonganti@101:         'amrfinderplus_run': [
kkonganti@101:             clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}",
kkonganti@101:             cliflag: null,
kkonganti@101:             clivalue: null
kkonganti@101:         ],
kkonganti@101:         'amrfinderplus_db': [
kkonganti@101:             clihelp: 'Path to AMRFinderPlus database. Please note that ' +
kkonganti@101:                 ' the databases should be ready and formatted with blast for use. ' +
kkonganti@101:                 'Please read more at: ' +
kkonganti@101:                 'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' +
kkonganti@101:                 "Default: ${params.amrfinderplus_db}",
kkonganti@101:             cliflag: '--database',
kkonganti@101:             clivalue: (params.amrfinderplus_db ?: '')
kkonganti@101:         ],
kkonganti@101:         'amrfinderplus_genes': [
kkonganti@101:             clihelp: 'Add the plus genes to the report',
kkonganti@101:             cliflag: '--plus',
kkonganti@101:             clivalue: (params.amrfinderplus_genes ? ' ' : '')
kkonganti@101:         ]
kkonganti@101:     ]
kkonganti@101: 
kkonganti@101:     toolspecs.each {
kkonganti@101:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@101:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     return tool
kkonganti@101: }