kkonganti@0: def mlstHelp(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:         'mlst_run': [
kkonganti@0:             clihelp: "Run MLST tool. Default: ${params.mlst_run}",
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'mlst_legacy': [
kkonganti@0:             clihelp: "Use old legacy output with allele header row (requires --mlst_scheme). " +
kkonganti@0:                 "Default: ${params.mlst_legacy}",
kkonganti@0:             cliflag: '--legacy',
kkonganti@0:             clivalue: (params.mlst_legacy ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'mlst_scheme': [
kkonganti@0:             clihelp: "Don't autodetect, force this scheme on all inputs. " +
kkonganti@0:                 "Default: ${params.mlst_scheme}",
kkonganti@0:             cliflag: '--scheme',
kkonganti@0:             clivalue: (params.mlst_scheme ?: null)
kkonganti@0:         ],
kkonganti@0:         'mlst_minid': [
kkonganti@0:             clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " +
kkonganti@0:                 "Default: ${params.mlst_minid}",
kkonganti@0:             cliflag: '--minid',
kkonganti@0:             clivalue: (params.mlst_minid ?: 95)
kkonganti@0:         ],
kkonganti@0:         'mlst_mincov': [
kkonganti@0:             clihelp: 'DNA %cov to report partial allele at all [?].' +
kkonganti@0:                 "Default: ${params.mlst_mincov}",
kkonganti@0:             cliflag: '--mincov',
kkonganti@0:             clivalue: (params.mlst_mincov ?: 10)
kkonganti@0:         ],
kkonganti@0:         'mlst_minscore': [
kkonganti@0:             clihelp: 'Minumum score out of 100 to match a scheme.' +
kkonganti@0:                 "Default: ${params.mlst_minscore}",
kkonganti@0:             cliflag: '--minscore',
kkonganti@0:             clivalue: (params.mlst_minscore ?: 50)
kkonganti@0:         ],
kkonganti@0:         'mlst_datadir': [
kkonganti@0:             clihelp: 'PubMLST data directory. ' +
kkonganti@0:                 "Default: ${params.mlst_datadir}",
kkonganti@0:             cliflag: '--datadir',
kkonganti@0:             clivalue: (params.mlst_datadir ?: null)
kkonganti@0:         ],
kkonganti@0:         'mlst_blastdb': [
kkonganti@0:             clihelp: 'BLAST database directory. ' +
kkonganti@0:                 "Default: ${params.mlst_blastdb}",
kkonganti@0:             cliflag: '--blastdb',
kkonganti@0:             clivalue: (params.mlst_blastdb ?: null)
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }