kkonganti@17: // Help text for kma align within CPIPES.
kkonganti@17: 
kkonganti@17: def kmaalignHelp(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:         'kmaalign_run': [
kkonganti@17:             clihelp: 'Run kma tool. Default: ' +
kkonganti@17:                 (params.kmaalign_run ?: false),
kkonganti@17:             cliflag: null,
kkonganti@17:             clivalue: null
kkonganti@17:         ],
kkonganti@17:         'kmaalign_int': [
kkonganti@17:             clihelp: 'Input file has interleaved reads. ' +
kkonganti@17:                 " Default: ${params.kmaalign_int}",
kkonganti@17:             cliflag: '-int',
kkonganti@17:             clivalue: (params.kmaalign_int ? ' ' : '')
kkonganti@17:         ], 
kkonganti@17:         'kmaalign_ef': [
kkonganti@17:             clihelp: 'Output additional features. ' +
kkonganti@17:                 "Default: ${params.kmaalign_ef}",
kkonganti@17:             cliflag: '-ef',
kkonganti@17:             clivalue: (params.kmaalign_ef ? ' ' : '')
kkonganti@17:         ], 
kkonganti@17:         'kmaalign_vcf': [
kkonganti@17:             clihelp: 'Output vcf file. 2 to apply FT. ' +
kkonganti@17:                 "Default: ${params.kmaalign_vcf}",
kkonganti@17:             cliflag: '-vcf',
kkonganti@17:             clivalue: (params.kmaalign_vcf ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_sam': [
kkonganti@17:             clihelp: 'Output SAM, 4/2096 for mapped/aligned. ' +
kkonganti@17:                 "Default: ${params.kmaalign_sam}",
kkonganti@17:             cliflag: '-sam',
kkonganti@17:             clivalue: (params.kmaalign_sam ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_nc': [
kkonganti@17:             clihelp: 'No consensus file. ' +
kkonganti@17:                 "Default: ${params.kmaalign_nc}",
kkonganti@17:             cliflag: '-nc',
kkonganti@17:             clivalue: (params.kmaalign_nc ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_na': [
kkonganti@17:             clihelp: 'No aln file. ' +
kkonganti@17:                 "Default: ${params.kmaalign_na}",
kkonganti@17:             cliflag: '-na',
kkonganti@17:             clivalue: (params.kmaalign_na ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_nf': [
kkonganti@17:             clihelp: 'No frag file. ' +
kkonganti@17:                 "Default: ${params.kmaalign_nf}",
kkonganti@17:             cliflag: '-nf',
kkonganti@17:             clivalue: (params.kmaalign_nf ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_a': [
kkonganti@17:             clihelp: 'Output all template mappings. ' +
kkonganti@17:                 "Default: ${params.kmaalign_a}",
kkonganti@17:             cliflag: '-a',
kkonganti@17:             clivalue: (params.kmaalign_a ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_and': [
kkonganti@17:             clihelp: 'Use both -mrs and p-value on consensus. ' +
kkonganti@17:                 "Default: ${params.kmaalign_and}",
kkonganti@17:             cliflag: '-and',
kkonganti@17:             clivalue: (params.kmaalign_and ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_oa': [
kkonganti@17:             clihelp: 'Use neither -mrs or p-value on consensus. ' +
kkonganti@17:                 "Default: ${params.kmaalign_oa}",
kkonganti@17:             cliflag: '-oa',
kkonganti@17:             clivalue: (params.kmaalign_oa ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_bc': [
kkonganti@17:             clihelp: 'Minimum support to call bases. ' +
kkonganti@17:                 "Default: ${params.kmaalign_bc}",
kkonganti@17:             cliflag: '-bc',
kkonganti@17:             clivalue: (params.kmaalign_bc ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_bcNano': [
kkonganti@17:             clihelp: 'Altered indel calling for ONT data. ' +
kkonganti@17:                 "Default: ${params.kmaalign_bcNano}",
kkonganti@17:             cliflag: '-bcNano',
kkonganti@17:             clivalue: (params.kmaalign_bcNano ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_bcd': [
kkonganti@17:             clihelp: 'Minimum depth to call bases. ' +
kkonganti@17:                 "Default: ${params.kmaalign_bcd}",
kkonganti@17:             cliflag: '-bcd',
kkonganti@17:             clivalue: (params.kmaalign_bcd ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_bcg': [
kkonganti@17:             clihelp: 'Maintain insignificant gaps. ' +
kkonganti@17:                 "Default: ${params.kmaalign_bcg}",
kkonganti@17:             cliflag: '-bcg',
kkonganti@17:             clivalue: (params.kmaalign_bcg ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_ID': [
kkonganti@17:             clihelp: 'Minimum consensus ID. ' +
kkonganti@17:                 "Default: ${params.kmaalign_ID}",
kkonganti@17:             cliflag: '-ID',
kkonganti@17:             clivalue: (params.kmaalign_ID ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_md': [
kkonganti@17:             clihelp: 'Minimum depth. ' +
kkonganti@17:                 "Default: ${params.kmaalign_md}",
kkonganti@17:             cliflag: '-md',
kkonganti@17:             clivalue: (params.kmaalign_md ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_dense': [
kkonganti@17:             clihelp: 'Skip insertion in consensus. ' +
kkonganti@17:                 "Default: ${params.kmaalign_dense}",
kkonganti@17:             cliflag: '-dense',
kkonganti@17:             clivalue: (params.kmaalign_dense ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_ref_fsa': [
kkonganti@17:             clihelp: 'Use Ns on indels. ' +
kkonganti@17:                 "Default: ${params.kmaalign_ref_fsa}",
kkonganti@17:             cliflag: '-ref_fsa',
kkonganti@17:             clivalue: (params.kmaalign_ref_fsa ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_Mt1': [
kkonganti@17:             clihelp: 'Map everything to one template. ' +
kkonganti@17:                 "Default: ${params.kmaalign_Mt1}",
kkonganti@17:             cliflag: '-Mt1',
kkonganti@17:             clivalue: (params.kmaalign_Mt1 ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_1t1': [
kkonganti@17:             clihelp: 'Map one query to one template. ' +
kkonganti@17:                 "Default: ${params.kmaalign_1t1}",
kkonganti@17:             cliflag: '-1t1',
kkonganti@17:             clivalue: (params.kmaalign_1t1 ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_mrs': [
kkonganti@17:             clihelp: 'Minimum relative alignment score. ' +
kkonganti@17:                 "Default: ${params.kmaalign_mrs}",
kkonganti@17:             cliflag: '-mrs',
kkonganti@17:             clivalue: (params.kmaalign_mrs ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_mrc': [
kkonganti@17:             clihelp: 'Minimum query coverage. ' +
kkonganti@17:                 "Default: ${params.kmaalign_mrc}",
kkonganti@17:             cliflag: '-mrc',
kkonganti@17:             clivalue: (params.kmaalign_mrc ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_mp': [
kkonganti@17:             clihelp: 'Minimum phred score of trailing and leading bases. ' +
kkonganti@17:                 "Default: ${params.kmaalign_mp}",
kkonganti@17:             cliflag: '-mp',
kkonganti@17:             clivalue: (params.kmaalign_mp ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_mq': [
kkonganti@17:             clihelp: 'Set the minimum mapping quality. ' +
kkonganti@17:                 "Default: ${params.kmaalign_mq}",
kkonganti@17:             cliflag: '-mq',
kkonganti@17:             clivalue: (params.kmaalign_mq ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_eq': [
kkonganti@17:             clihelp: 'Minimum average quality score. ' +
kkonganti@17:                 "Default: ${params.kmaalign_eq}",
kkonganti@17:             cliflag: '-eq',
kkonganti@17:             clivalue: (params.kmaalign_eq ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_5p': [
kkonganti@17:             clihelp: 'Trim 5 prime by this many bases. ' +
kkonganti@17:                 "Default: ${params.kmaalign_5p}",
kkonganti@17:             cliflag: '-5p',
kkonganti@17:             clivalue: (params.kmaalign_5p ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_3p': [
kkonganti@17:             clihelp: 'Trim 3 prime by this many bases ' +
kkonganti@17:                 "Default: ${params.kmaalign_3p}",
kkonganti@17:             cliflag: '-3p',
kkonganti@17:             clivalue: (params.kmaalign_3p ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_apm': [
kkonganti@17:             clihelp: 'Sets both -pm and -fpm ' +
kkonganti@17:                 "Default: ${params.kmaalign_apm}",
kkonganti@17:             cliflag: '-apm',
kkonganti@17:             clivalue: (params.kmaalign_apm ?: '')
kkonganti@17:         ],
kkonganti@17:         'kmaalign_cge': [
kkonganti@17:             clihelp: 'Set CGE penalties and rewards ' +
kkonganti@17:                 "Default: ${params.kmaalign_cge}",
kkonganti@17:             cliflag: '-cge',
kkonganti@17:             clivalue: (params.kmaalign_cge ? ' ' : '')
kkonganti@17:         ],
kkonganti@17: 
kkonganti@17:     ]
kkonganti@17: 
kkonganti@17:     toolspecs.each {
kkonganti@17:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     return tool
kkonganti@17: }