kkonganti@92: // Help text for kraken2 within CPIPES.
kkonganti@92: 
kkonganti@92: def kraken2Help(params) {
kkonganti@92: 
kkonganti@92:     Map tool = [:]
kkonganti@92:     Map toolspecs = [:]
kkonganti@92:     tool.text = [:]
kkonganti@92:     tool.helpparams = [:]
kkonganti@92: 
kkonganti@92:     toolspecs = [
kkonganti@92:         'kraken2_db': [
kkonganti@92:             clihelp: "Absolute path to kraken database. Default: ${params.kraken2_db}",
kkonganti@92:             cliflag: '--db',
kkonganti@92:             clivalue: null
kkonganti@92:         ],
kkonganti@92:         'kraken2_confidence': [
kkonganti@92:             clihelp: 'Confidence score threshold which must be ' +
kkonganti@92:                 "between 0 and 1. Default: ${params.kraken2_confidence}",
kkonganti@92:             cliflag: '--confidence',
kkonganti@92:             clivalue: (params.kraken2_confidence ?: '')
kkonganti@92:         ],
kkonganti@92:         'kraken2_quick': [
kkonganti@92:             clihelp: "Quick operation (use first hit or hits). Default: ${params.kraken2_quick}",
kkonganti@92:             cliflag: '--quick',
kkonganti@92:             clivalue: (params.kraken2_quick ? ' ' : '')
kkonganti@92:         ],
kkonganti@92:         'kraken2_use_mpa_style': [
kkonganti@92:             clihelp: "Report output like Kraken 1's " +
kkonganti@92:                 "kraken-mpa-report. Default: ${params.kraken2_use_mpa_style}",
kkonganti@92:             cliflag: '--use-mpa-style',
kkonganti@92:             clivalue: (params.kraken2_use_mpa_style ? ' ' : '')
kkonganti@92:         ],
kkonganti@92:         'kraken2_minimum_base_quality': [
kkonganti@92:             clihelp: 'Minimum base quality used in classification ' +
kkonganti@92:                 " which is only effective with FASTQ input. Default: ${params.kraken2_minimum_base_quality}",
kkonganti@92:             cliflag: '--minimum-base-quality',
kkonganti@92:             clivalue: (params.kraken2_minimum_base_quality ?: '')
kkonganti@92:         ],
kkonganti@92:         'kraken2_report_zero_counts': [
kkonganti@92:             clihelp: 'Report counts for ALL taxa, even if counts are zero. ' +
kkonganti@92:                 "Default: ${params.kraken2_report_zero_counts}",
kkonganti@92:             cliflag: '--report-zero-counts',
kkonganti@92:             clivalue: (params.kraken2_report_zero_counts ? ' ' : '')
kkonganti@92:         ],
kkonganti@92:         'kraken2_report_minmizer_data': [
kkonganti@92:             clihelp: 'Report minimizer and distinct minimizer count' +
kkonganti@92:                 ' information in addition to normal Kraken report. ' +
kkonganti@92:                 "Default: ${params.kraken2_report_minimizer_data}",
kkonganti@92:             cliflag: '--report-minimizer-data',
kkonganti@92:             clivalue: (params.kraken2_report_minimizer_data ? ' ' : '')
kkonganti@92:         ],
kkonganti@92:         'kraken2_use_names': [
kkonganti@92:             clihelp: 'Print scientific names instead of just taxids. ' +
kkonganti@92:                 "Default: ${params.kraken2_use_names}",
kkonganti@92:             cliflag: '--use-names',
kkonganti@92:             clivalue: (params.kraken2_use_names ? ' ' : '')
kkonganti@92:         ],
kkonganti@92:         'kraken2_extract_bug': [
kkonganti@92:             clihelp: 'Extract the reads or contigs beloging to this bug. ' +
kkonganti@92:                 "Default: ${params.kraken2_extract_bug}",
kkonganti@92:             cliflag: null,
kkonganti@92:             clivalue: null
kkonganti@92:         ]
kkonganti@92:     ]
kkonganti@92: 
kkonganti@92:     toolspecs.each {
kkonganti@92:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@92:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@92:     }
kkonganti@92: 
kkonganti@92:     return tool
kkonganti@92: }