kkonganti@17: // Help text for get_top_unique_mash_hit_genomes.py (tuspy) within CPIPES.
kkonganti@17: 
kkonganti@17: def tuspyHelp(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:         'tuspy_run': [
kkonganti@17:             clihelp: 'Run the get_top_unique_mash_hits_genomes.py ' +
kkonganti@17:                 'script. Default: ' +
kkonganti@17:                 (params.tuspy_run ?: false),
kkonganti@17:             cliflag: null,
kkonganti@17:             clivalue: null
kkonganti@17:         ],
kkonganti@17:         'tuspy_s': [
kkonganti@17:             clihelp: 'Absolute UNIX path to metadata text file with the ' +
kkonganti@17:                 'field separator, | and ' +
kkonganti@17:                 '5 fields: serotype|asm_lvl|asm_url|snp_cluster_id' +
kkonganti@17:                 'Ex: serotype=Derby,antigen_formula=4:f,g:-|Scaffold|402440|ftp://...' +
kkonganti@17:                 '|PDS000096654.2. Mentioning this option will create a pickle file for the ' +
kkonganti@17:                 'provided metadata and exits.' +
kkonganti@17:                 " Default: ${params.tuspy_s}",
kkonganti@17:             cliflag: '-s',
kkonganti@17:             clivalue: (params.tuspy_s ?: '')
kkonganti@17:         ],
kkonganti@17:         'tuspy_m': [
kkonganti@17:             clihelp: 'Absolute UNIX path to mash screen results file.' +
kkonganti@17:                 " Default: ${params.tuspy_m}",
kkonganti@17:             cliflag: '-m',
kkonganti@17:             clivalue: (params.tuspy_m ?: '')
kkonganti@17:         ],
kkonganti@17:         'tuspy_ps': [
kkonganti@17:             clihelp: 'Absolute UNIX Path to serialized metadata object ' +
kkonganti@17:                 'in a pickle file.' +
kkonganti@17:                 " Default: ${params.tuspy_ps}",
kkonganti@17:             cliflag: '-ps',
kkonganti@17:             clivalue: (params.tuspy_ps ?: '')
kkonganti@17:         ],
kkonganti@17:         'tuspy_gd': [
kkonganti@17:             clihelp: 'Absolute UNIX Path to directory containing ' +
kkonganti@17:                 'gzipped genome FASTA files.' +
kkonganti@17:                 " Default: ${params.tuspy_gd}",
kkonganti@17:             cliflag: '-gd',
kkonganti@17:             clivalue: (params.tuspy_gd ?: '')
kkonganti@17:         ],
kkonganti@17:         'tuspy_gds': [
kkonganti@17:             clihelp: 'Genome FASTA file suffix to search for in the ' +
kkonganti@17:                 'genome directory.' +
kkonganti@17:                 " Default: ${params.tuspy_gds}",
kkonganti@17:             cliflag: '-gds',
kkonganti@17:             clivalue: (params.tuspy_gds ?: '')
kkonganti@17:         ],
kkonganti@17:         'tuspy_n': [
kkonganti@17:             clihelp: 'Return up to this many number of top N unique ' +
kkonganti@17:                 'genome accession hits.' +
kkonganti@17:                 " Default: ${params.tuspy_n}",
kkonganti@17:             cliflag: '-n',
kkonganti@17:             clivalue: (params.tuspy_n ?: '')
kkonganti@17:         ],
kkonganti@17:         'tuspy_skip': [
kkonganti@17:             clihelp: 'Skip all hits which belong to the following bioproject ' +
kkonganti@17:                 'accession(s). A comma separated list of more than one bioproject. ' +
kkonganti@17:                 " Default: ${params.tuspy_skip}",
kkonganti@17:             cliflag: '-skip',
kkonganti@17:             clivalue: (params.tuspy_skip ?: '')
kkonganti@17:         ]
kkonganti@17:     ]
kkonganti@17: 
kkonganti@17:     toolspecs.each {
kkonganti@17:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     return tool
kkonganti@17: }