kkonganti@0: // Help text for `gen_salmon_tph_and_krona_tsv.py` (gsalkronapy) within CPIPES.
kkonganti@0: 
kkonganti@0: def gsalkronapyHelp(params) {
kkonganti@0: 
kkonganti@0:     Map tool = [:]
kkonganti@0:     Map toolspecs = [:]
kkonganti@0:     tool.text = [:]
kkonganti@0:     tool.helpparams = [:]
kkonganti@0: 
kkonganti@0:     toolspecs = [
kkonganti@0:         'gsalkronapy_run': [
kkonganti@0:             clihelp: 'Run the `gen_salmon_tph_and_krona_tsv.py` script. Default: ' +
kkonganti@0:                 (params.gsalkronapy_run ?: false),
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'gsalkronapy_sf': [
kkonganti@0:             clihelp: 'Set the scaling factor by which TPM values ' +
kkonganti@0:                 'are scaled down.' +
kkonganti@0:                 " Default: ${params.gsalkronapy_sf}",
kkonganti@0:             cliflag: '-sf',
kkonganti@0:             clivalue: (params.gsalkronapy_sf ?: '')
kkonganti@0:         ],
kkonganti@0:         'gsalkronapy_smres_suffix': [
kkonganti@0:             clihelp: 'Find the `sourmash gather` result files ' +
kkonganti@0:                 'ending in this suffix.' +
kkonganti@0:                 " Default: ${params.gsalkronapy_smres_suffix}",
kkonganti@0:             cliflag: '-smres-suffix',
kkonganti@0:             clivalue: (params.gsalkronapy_smres_suffix ?: '')
kkonganti@0:         ],
kkonganti@0:         'gsalkronapy_failed_suffix': [
kkonganti@0:             clihelp: 'Find the sample names which failed classification stored ' +
kkonganti@0:                 'inside the files ending in this suffix.' +
kkonganti@0:                 " Default: ${params.gsalkronapy_failed_suffix}",
kkonganti@0:             cliflag: '-failed-suffix',
kkonganti@0:             clivalue: (params.gsalkronapy_failed_suffix ?: '')
kkonganti@0:         ],
kkonganti@0:         'gsalkronapy_num_lin_cols': [
kkonganti@0:             clihelp: 'Number of columns expected in the lineages CSV file. ' +
kkonganti@0:                 " Default: ${params.gsalkronapy_num_lin_cols}",
kkonganti@0:             cliflag: '-num-lin-cols',
kkonganti@0:             clivalue: (params.gsalkronapy_num_lin_cols ?: '')
kkonganti@0:         ],
kkonganti@0:         'gsalkronapy_lin_regex': [
kkonganti@0:             clihelp: 'Number of columns expected in the lineages CSV file. ' +
kkonganti@0:                 " Default: ${params.gsalkronapy_num_lin_cols}",
kkonganti@0:             cliflag: '-num-lin-cols',
kkonganti@0:             clivalue: (params.gsalkronapy_num_lin_cols ?: '')
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }