kkonganti@0: // Help text for mash screen within CPIPES.
kkonganti@0: 
kkonganti@0: def mashscreenHelp(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:         'mashscreen_run': [
kkonganti@0:             clihelp: 'Run `mash screen` tool. Default: ' +
kkonganti@0:                 (params.mashscreen_run ?: false),
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'mashscreen_w': [
kkonganti@0:             clihelp: 'Winner-takes-all strategy for identity estimates. After counting ' +
kkonganti@0:                 'hashes for each query, hashes that appear in multiple queries will ' +
kkonganti@0:                 'be removed from all except the one with the best identity (ties ' +
kkonganti@0:                 'broken by larger query), and other identities will be reduced. This ' +
kkonganti@0:                 'removes output redundancy, providing a rough compositional outline. ' +
kkonganti@0:                 " Default: ${params.mashscreen_w}",
kkonganti@0:             cliflag: '-w',
kkonganti@0:             clivalue: (params.mashscreen_w ? ' ' : '')
kkonganti@0:         ], 
kkonganti@0:         'mashscreen_i': [
kkonganti@0:             clihelp: 'Minimum identity to report. Inclusive unless set to zero, in which ' +
kkonganti@0:                 'case only identities greater than zero (i.e. with at least one ' +
kkonganti@0:                 'shared hash) will be reported. Set to -1 to output everything. ' +
kkonganti@0:                 "(-1-1). Default: ${params.mashscreen_i}",
kkonganti@0:             cliflag: '-i',
kkonganti@0:             clivalue: (params.mashscreen_i ?: '')
kkonganti@0:         ],
kkonganti@0:         'mashscreen_v': [
kkonganti@0:             clihelp: 'Maximum p-value to report (0-1). ' +
kkonganti@0:                 "Default: ${params.mashscreen_v}",
kkonganti@0:             cliflag: '-v',
kkonganti@0:             clivalue: (params.mashscreen_v ?: '')
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }