kkonganti@11: // Help text for `polypolish within CPIPES.
kkonganti@11: 
kkonganti@11: def polypolishHelp(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:         'polypolish_run': [
kkonganti@11:             clihelp: 'Run polypolish tool. Default: ' +
kkonganti@11:                 (params.polypolish_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'polypolish_d': [
kkonganti@11:             clihelp: 'A base must occur at least this many times in the pileup to be considered valid. ' +
kkonganti@11:                 "Default: ${params.polypolish_d}",
kkonganti@11:             cliflag: '-d',
kkonganti@11:             clivalue: (params.polypolish_d ?: '')
kkonganti@11:         ],
kkonganti@11:         'polypolish_i': [
kkonganti@11:             clihelp: 'A base must make up less than this fraction of the read depth to be considered invalid. ' +
kkonganti@11:                 "Default: ${params.polypolish_i}",
kkonganti@11:             cliflag: '-i',
kkonganti@11:             clivalue: (params.polypolish_i ?: '')
kkonganti@11:         ],
kkonganti@11:         'polypolish_m': [
kkonganti@11:             clihelp: 'Ignore alignments with more than this many mismatches and indels. ' +
kkonganti@11:                 "Default: ${params.polypolish_m}",
kkonganti@11:             cliflag: '-m',
kkonganti@11:             clivalue: (params.polypolish_m ?: '')
kkonganti@11:         ],
kkonganti@11:         'polypolish_v': [
kkonganti@11:             clihelp: 'A base must make up at least this fraction of the read depth to be considered valid. ' +
kkonganti@11:                 "Default: ${params.polypolish_v}",
kkonganti@11:             cliflag: '-v',
kkonganti@11:             clivalue: (params.polypolish_v ?: '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }