kkonganti@0: // Help text for sourmash gather within CPIPES.mashsketch
kkonganti@0: 
kkonganti@0: def sourmashgatherHelp(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:         'sourmashgather_run': [
kkonganti@0:             clihelp: 'Run `sourmash gather` tool. Default: ' +
kkonganti@0:                 (params.sourmashgather_run ?: false),
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_n': [
kkonganti@0:             clihelp: 'Number of results to report. ' +
kkonganti@0:                 'By default, will terminate at --sourmashgather_thr_bp value. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_n}",
kkonganti@0:             cliflag: '-n',
kkonganti@0:             clivalue: (params.sourmashgather_n ?: '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_thr_bp': [
kkonganti@0:             clihelp: 'Reporting threshold (in bp) for estimated overlap with remaining query. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_thr_bp}",
kkonganti@0:             cliflag: '--threshold-bp',
kkonganti@0:             clivalue: (params.sourmashgather_thr_bp ?: '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_ani_ci': [
kkonganti@0:             clihelp: 'Output confidence intervals for ANI estimates. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_ani_ci}",
kkonganti@0:             cliflag: '--estimate-ani-ci',
kkonganti@0:             clivalue: (params.sourmashgather_ani_ci ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_k': [
kkonganti@0:             clihelp: 'The k-mer size to select. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_k}",
kkonganti@0:             cliflag: '-k',
kkonganti@0:             clivalue: (params.sourmashgather_k ?: '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_dna': [
kkonganti@0:             clihelp: 'Choose DNA signature. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_dna}",
kkonganti@0:             cliflag: '--dna',
kkonganti@0:             clivalue: (params.sourmashgather_dna ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_rna': [
kkonganti@0:             clihelp: 'Choose RNA signature. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_rna}",
kkonganti@0:             cliflag: '--rna',
kkonganti@0:             clivalue: (params.sourmashgather_rna ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_nuc': [
kkonganti@0:             clihelp: 'Choose Nucleotide signature. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_nuc}",
kkonganti@0:             cliflag: '--nucleotide',
kkonganti@0:             clivalue: (params.sourmashgather_nuc ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_scaled': [
kkonganti@0:             clihelp: 'Scaled value should be between 100 and 1e6. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_scaled}",
kkonganti@0:             cliflag: '--scaled',
kkonganti@0:             clivalue: (params.sourmashgather_scaled ?: '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_inc_pat': [
kkonganti@0:             clihelp: 'Search only signatures that match this pattern in name, filename, or md5. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_inc_pat}",
kkonganti@0:             cliflag: '--include-db-pattern',
kkonganti@0:             clivalue: (params.sourmashgather_inc_pat ?: '')
kkonganti@0:         ],
kkonganti@0:         'sourmashgather_exc_pat': [
kkonganti@0:             clihelp: 'Search only signatures that do not match this pattern in name, filename, or md5. ' +
kkonganti@0:                 "Default: ${params.sourmashgather_exc_pat}",
kkonganti@0:             cliflag: '--exclude-db-pattern',
kkonganti@0:             clivalue: (params.sourmashgather_exc_pat ?: '')
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }