kkonganti@0: def amrfinderplusHelp(params) { kkonganti@0: kkonganti@0: Map tool = [:] kkonganti@0: Map toolspecs = [:] kkonganti@0: tool.text = [:] kkonganti@0: tool.helpparams = [:] kkonganti@0: kkonganti@0: toolspecs = [ kkonganti@0: 'amrfinderplus_run': [ kkonganti@0: clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}", kkonganti@0: cliflag: null, kkonganti@0: clivalue: null kkonganti@0: ], kkonganti@0: 'amrfinderplus_db': [ kkonganti@0: clihelp: 'Path to AMRFinderPlus database. Please note that ' + kkonganti@0: ' the databases should be ready and formatted with blast for use. ' + kkonganti@0: 'Please read more at: ' + kkonganti@0: 'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' + kkonganti@0: "Default: ${params.amrfinderplus_db}", kkonganti@0: cliflag: '--database', kkonganti@0: clivalue: (params.amrfinderplus_db ?: '') kkonganti@0: ], kkonganti@0: 'amrfinderplus_genes': [ kkonganti@0: clihelp: 'Add the plus genes to the report', kkonganti@0: cliflag: '--plus', kkonganti@0: clivalue: (params.amrfinderplus_genes ? ' ' : '') kkonganti@0: ] kkonganti@0: ] kkonganti@0: kkonganti@0: toolspecs.each { kkonganti@0: k, v -> tool.text['--' + k] = "${v.clihelp}" kkonganti@0: tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] kkonganti@0: } kkonganti@0: kkonganti@0: return tool kkonganti@0: }