kkonganti@1: // Help text for sourmash_filter_hits.py (sfhpy) within CPIPES.
kkonganti@1: def sfhpyHelp(params) {
kkonganti@1: 
kkonganti@1:     Map tool = [:]
kkonganti@1:     Map toolspecs = [:]
kkonganti@1:     tool.text = [:]
kkonganti@1:     tool.helpparams = [:]
kkonganti@1: 
kkonganti@1:     toolspecs = [
kkonganti@1:         'sfhpy_run': [
kkonganti@1:             clihelp: 'Run the sourmash_filter_hits.py ' +
kkonganti@1:                 'script. Default: ' +
kkonganti@1:                 (params.sfhpy_run ?: false),
kkonganti@1:             cliflag: null,
kkonganti@1:             clivalue: null
kkonganti@1:         ],
kkonganti@1:         'sfhpy_fcn': [
kkonganti@1:             clihelp: 'Column name by which filtering of rows should be applied. ' +
kkonganti@1:                 "Default: ${params.sfhpy_fcn}",
kkonganti@1:             cliflag: '-fcn',
kkonganti@1:             clivalue: (params.sfhpy_fcn ?: '')
kkonganti@1:         ],
kkonganti@1:         'sfhpy_fcv': [
kkonganti@1:             clihelp: 'Remove genomes whose match with the query FASTQ is less than ' +
kkonganti@1:                 'this much. ' +
kkonganti@1:                 "Default: ${params.sfhpy_fcv}",
kkonganti@1:             cliflag: '-fcv',
kkonganti@1:             clivalue: (params.sfhpy_fcv ?: '')
kkonganti@1:         ],
kkonganti@1:         'sfhpy_gt': [
kkonganti@1:             clihelp: 'Apply greather than or equal to condition on numeric values of ' +
kkonganti@1:                 '--sfhpy_fcn column. ' +
kkonganti@1:                 "Default: ${params.sfhpy_gt}",
kkonganti@1:             cliflag: '-gt',
kkonganti@1:             clivalue: (params.sfhpy_gt ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sfhpy_lt': [
kkonganti@1:             clihelp: 'Apply less than or equal to condition on numeric values of ' +
kkonganti@1:                 '--sfhpy_fcn column. ' +
kkonganti@1:                 "Default: ${params.sfhpy_lt}",
kkonganti@1:             cliflag: '-gt',
kkonganti@1:             clivalue: (params.sfhpy_lt ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:     ]
kkonganti@1: 
kkonganti@1:     toolspecs.each {
kkonganti@1:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@1:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     return tool
kkonganti@1: }