kkonganti@11: // Help text for ktImportText (krona) within CPIPES.
kkonganti@11: 
kkonganti@11: def kronaktimporttextHelp(params) {
kkonganti@11: 
kkonganti@11:     Map tool = [:]
kkonganti@11:     Map toolspecs = [:]
kkonganti@11:     tool.text = [:]
kkonganti@11:     tool.helpparams = [:]
kkonganti@11: 
kkonganti@11:     toolspecs = [
kkonganti@11:         'krona_ktIT_run': [
kkonganti@11:             clihelp: 'Run the ktImportText (ktIT) from krona. Default: ' +
kkonganti@11:                 (params.krona_ktIT_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'krona_ktIT_n': [
kkonganti@11:             clihelp: 'Name of the highest level. ' +
kkonganti@11:                 "Default: ${params.krona_ktIT_n}",
kkonganti@11:             cliflag: '-n',
kkonganti@11:             clivalue: (params.krona_ktIT_n ?: '')
kkonganti@11:         ],
kkonganti@11:         'krona_ktIT_q': [
kkonganti@11:             clihelp: 'Input file(s) do not have a field for quantity. ' +
kkonganti@11:                 "Default: ${params.krona_ktIT_q}",
kkonganti@11:             cliflag: '-q',
kkonganti@11:             clivalue: (params.krona_ktIT_q ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'krona_ktIT_c': [
kkonganti@11:             clihelp: 'Combine data from each file, rather than creating separate datasets '
kkonganti@11:                 + 'within the chart. ' +
kkonganti@11:                 "Default: ${params.krona_ktIT_c}",
kkonganti@11:             cliflag: '-c',
kkonganti@11:             clivalue: (params.krona_ktIT_c ? ' ' : '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }