kkonganti@11: // Help text for dl_pubmlst_profiles_and_schemes.py (dpubmlstpy) within CPIPES.
kkonganti@11: 
kkonganti@11: def dpubmlstpyHelp(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:         'dpubmlstpy_run': [
kkonganti@11:             clihelp: 'Run the dl_pubmlst_profiles_and_schemes.py ' +
kkonganti@11:                 'script. Default: ' +
kkonganti@11:                 (params.dpubmlstpy_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'dpubmlstpy_org': [
kkonganti@11:             clihelp: 'The organism name to download the MLST alleles ' +
kkonganti@11:                 'FASTA and profile CSV for. ' +
kkonganti@11:                 " Default: ${params.dpubmlstpy_org}",
kkonganti@11:             cliflag: '-org',
kkonganti@11:             clivalue: (params.dpubmlstpy_org ?: '')
kkonganti@11:         ],
kkonganti@11:         'dpubmlstpy_mlsts': [
kkonganti@11:             clihelp: 'The MLST scheme ID to download. ' +
kkonganti@11:                 " Default: ${params.dpubmlstpy_mlsts}",
kkonganti@11:             cliflag: '-mlsts',
kkonganti@11:             clivalue: (params.dpubmlstpy_mlsts ?: '')
kkonganti@11:         ],
kkonganti@11:         'dpubmlstpy_profile': [
kkonganti@11:             clihelp: 'The MLST profile name in the scheme. ' +
kkonganti@11:                 " Default: ${params.dpubmlstpy_profile}",
kkonganti@11:             cliflag: '-profile',
kkonganti@11:             clivalue: (params.dpubmlstpy_profile ?: '')
kkonganti@11:         ],
kkonganti@11:         'dpubmlstpy_loci': [
kkonganti@11:             clihelp: 'The key name in the JSON response which lists the ' +
kkonganti@11:                 'allele URLs to download. ' +
kkonganti@11:                 " Default: ${params.dpubmlstpy_loci}",
kkonganti@11:             cliflag: '-loci',
kkonganti@11:             clivalue: (params.dpubmlstpy_loci ?: '')
kkonganti@11:         ],
kkonganti@11:         'dpubmlstpy_suffix': [
kkonganti@11:             clihelp: 'What should be the suffix of the downloaded allele ' +
kkonganti@11:                 'FASTA. ' +
kkonganti@11:                 " Default: ${params.dpubmlstpy_suffix}",
kkonganti@11:             cliflag: '-suffix',
kkonganti@11:             clivalue: (params.dpubmlstpy_suffix ?: '')
kkonganti@11:         ],
kkonganti@11:         'dpubmlstpy_akey': [
kkonganti@11:             clihelp: 'What is the key in the JSON response that contains ' +
kkonganti@11:                 'the URL for allele FASTA. ' +
kkonganti@11:                 " Default: ${params.dpubmlstpy_akey}",
kkonganti@11:             cliflag: '-akey',
kkonganti@11:             clivalue: (params.dpubmlstpy_akey ?: '')
kkonganti@11:         ],
kkonganti@11:         'dpubmlstpy_id': [
kkonganti@11:             clihelp: 'What is the key in the JSON response that contains ' +
kkonganti@11:                 'the name of the allele FASTA. ' +
kkonganti@11:                 " Default: ${params.dpubmlstpy_id}",
kkonganti@11:             cliflag: '-id',
kkonganti@11:             clivalue: (params.dpubmlstpy_id ?: '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }