kkonganti@17: // Help text for abricate within CPIPES.
kkonganti@17: 
kkonganti@17: def abricateHelp(params) {
kkonganti@17: 
kkonganti@17:     Map tool = [:]
kkonganti@17:     Map toolspecs = [:]
kkonganti@17:     tool.text = [:]
kkonganti@17:     tool.helpparams = [:]
kkonganti@17: 
kkonganti@17:     toolspecs = [
kkonganti@17:         'abricate_run': [
kkonganti@17:             clihelp: 'Run ABRicate tool. Default: ' +
kkonganti@17:                 (params.abricate_run ?: false),
kkonganti@17:             cliflag: null,
kkonganti@17:             clivalue: null
kkonganti@17:         ],
kkonganti@17:         'abricate_minid': [
kkonganti@17:             clihelp: 'Minimum DNA %identity. ' +
kkonganti@17:                 "Default: " + (params.abricate_minid ?: 80),
kkonganti@17:             cliflag: '--minid',
kkonganti@17:             clivalue: (params.abricate_minid ?: 80)
kkonganti@17:         ], 
kkonganti@17:         'abricate_mincov': [
kkonganti@17:             clihelp: 'Minimum DNA %coverage. ' +
kkonganti@17:                 "Default: " + (params.abricate_mincov ?: 80),
kkonganti@17:             cliflag: '--mincov',
kkonganti@17:             clivalue: (params.abricate_mincov ?: 80)
kkonganti@17:         ],
kkonganti@17:         'abricate_datadir': [
kkonganti@17:             clihelp: 'ABRicate databases folder. ' +
kkonganti@17:                 "Default: " + (params.abricate_datadir ?: 'undefined'),
kkonganti@17:             cliflag: '--datadir',
kkonganti@17:             clivalue: (params.abricate_datadir ?: '')
kkonganti@17:         ]
kkonganti@17:     ]
kkonganti@17: 
kkonganti@17:     toolspecs.each {
kkonganti@17:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     return tool
kkonganti@17: }