kkonganti@11: // Help text for checkm2 predict within CPIPES.
kkonganti@11: 
kkonganti@11: def checkm2predictHelp(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:         'checkm2predict_run': [
kkonganti@11:             clihelp: 'Run `checkm2 predict` tool. Default: ' +
kkonganti@11:                 (params.checkm2predict_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_quiet': [
kkonganti@11:             clihelp: 'Only output errors. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_quiet}",
kkonganti@11:             cliflag: '--quiet',
kkonganti@11:             clivalue: (params.checkm2predict_quiet ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_lowmem': [
kkonganti@11:             clihelp: 'Low memory mode. Reduces DIAMOND blocksize to ' +
kkonganti@11:                 'significantly reduce RAM usage at the expense of longer runtime. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_lowmem}",
kkonganti@11:             cliflag: '--lowmem',
kkonganti@11:             clivalue: (params.checkm2predict_lowmem ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_general': [
kkonganti@11:             clihelp: 'Force the use of the general quality prediction model (gradient boost). ' +
kkonganti@11:                 "Default: ${params.checkm2predict_general}",
kkonganti@11:             cliflag: '--general',
kkonganti@11:             clivalue: (params.checkm2predict_general ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_specific': [
kkonganti@11:             clihelp: "Force the use of the specific quality prediction model (neural network) " +
kkonganti@11:                 "Default: ${params.checkm2predict_specific}",
kkonganti@11:             cliflag: '--specific',
kkonganti@11:             clivalue: (params.checkm2predict_specific ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_allmodels': [
kkonganti@11:             clihelp: 'Output quality prediction for both models for each genome. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_allmodels}",
kkonganti@11:             cliflag: '--allmodels',
kkonganti@11:             clivalue: (params.checkm2predict_allmodels ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_genes': [
kkonganti@11:             clihelp: 'Treat input files as protein files. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_genes}",
kkonganti@11:             cliflag: '--genes',
kkonganti@11:             clivalue: (params.checkm2predict_genes ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_x': [
kkonganti@11:             clihelp: 'Extension of input files. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_x}",
kkonganti@11:             cliflag: '-x',
kkonganti@11:             clivalue: (params.checkm2predict_x ?: '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_tmpdir': [
kkonganti@11:             clihelp: 'Specify an alternate directory for temporary files. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_tmpdir}",
kkonganti@11:             cliflag: '--tmpdir',
kkonganti@11:             clivalue: (params.checkm2predict_tmpdir ?: '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_rminterfiles': [
kkonganti@11:             clihelp: 'Remove all intermediate files (protein files, diamond output). ' +
kkonganti@11:                 "Default: ${params.checkm2predict_rminterfiles}",
kkonganti@11:             cliflag: '--remove_intermediates',
kkonganti@11:             clivalue: (params.checkm2predict_rminterfiles ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_ttable': [
kkonganti@11:             clihelp: 'Provide a specific progidal translation table for bins. The default ' +
kkonganti@11:                 'value of false will automatically determine either 11 or 4. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_ttable}",
kkonganti@11:             cliflag: '--ttable',
kkonganti@11:             clivalue: (params.checkm2predict_ttable ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_dbg_cos': [
kkonganti@11:             clihelp: 'DEBUG: Write cosine similarity values to a file. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_dbg_cos}",
kkonganti@11:             cliflag: '--dbg_cos',
kkonganti@11:             clivalue: (params.checkm2predict_dbg_cos ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'checkm2predict_dbg_vectors': [
kkonganti@11:             clihelp: 'DEBUG: Write Dump pickled feature vectors to a file. ' +
kkonganti@11:                 "Default: ${params.checkm2predict_dbg_vectors}",
kkonganti@11:             cliflag: '--dbg_vectors',
kkonganti@11:             clivalue: (params.checkm2predict_dbg_vectors ? ' ' : '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }