kkonganti@0: // Help text for `masurca's polca.sh` within CPIPES.
kkonganti@0: 
kkonganti@0: def masurcapolcaHelp(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:         'masurcapolca_run': [
kkonganti@0:             clihelp: 'Run `polca.sh` from masurca. Default: ' +
kkonganti@0:                 (params.masurcapolca_run ?: false),
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'masurcapolca_n': [
kkonganti@0:             clihelp: 'Do not polish, just create vcf file, evaluate the assembly and exit. ' +
kkonganti@0:                 "Default: ${params.masurcapolca_n}",
kkonganti@0:             cliflag: '-n',
kkonganti@0:             clivalue: (params.masurcapolca_n ? ' ' : '')
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }