kkonganti@101: def mlstHelp(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:         'mlst_run': [
kkonganti@101:             clihelp: "Run MLST tool. Default: ${params.mlst_run}",
kkonganti@101:             cliflag: null,
kkonganti@101:             clivalue: null
kkonganti@101:         ],
kkonganti@101:         'mlst_minid': [
kkonganti@101:             clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " +
kkonganti@101:                 "Default: ${params.mlst_minid}",
kkonganti@101:             cliflag: '--minid',
kkonganti@101:             clivalue: (params.mlst_minid ?: 95)
kkonganti@101:         ],
kkonganti@101:         'mlst_mincov': [
kkonganti@101:             clihelp: 'DNA %cov to report partial allele at all [?].' +
kkonganti@101:                 "Default: ${params.mlst_mincov}",
kkonganti@101:             cliflag: '--mincov',
kkonganti@101:             clivalue: (params.mlst_mincov ?: 10)
kkonganti@101:         ],
kkonganti@101:         'mlst_minscore': [
kkonganti@101:             clihelp: 'Minumum score out of 100 to match a scheme.' +
kkonganti@101:                 "Default: ${params.mlst_minscore}",
kkonganti@101:             cliflag: '--minscore',
kkonganti@101:             clivalue: (params.mlst_minscore ?: 50)
kkonganti@101:         ]
kkonganti@101:     ]
kkonganti@101: 
kkonganti@101:     toolspecs.each {
kkonganti@101:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@101:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     return tool
kkonganti@101: }