kkonganti@17: // Help text for sourmash gather within CPIPES.
kkonganti@17: 
kkonganti@17: def sourmashgatherHelp(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:         'sourmashgather_run': [
kkonganti@17:             clihelp: 'Run `sourmash gather` tool. Default: ' +
kkonganti@17:                 (params.sourmashgather_run ?: false),
kkonganti@17:             cliflag: null,
kkonganti@17:             clivalue: null
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_n': [
kkonganti@17:             clihelp: 'Number of results to report. ' +
kkonganti@17:                 'By default, will terminate at --sourmashgather_thr_bp value. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_n}",
kkonganti@17:             cliflag: '-n',
kkonganti@17:             clivalue: (params.sourmashgather_n ?: '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_thr_bp': [
kkonganti@17:             clihelp: 'Reporting threshold (in bp) for estimated overlap with remaining query. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_thr_bp}",
kkonganti@17:             cliflag: '--threshold-bp',
kkonganti@17:             clivalue: (params.sourmashgather_thr_bp ?: '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_ignoreabn': [
kkonganti@17:             clihelp: 'Do NOT use k-mer abundances if present. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_ignoreabn}",
kkonganti@17:             cliflag: '--ignore-abundance',
kkonganti@17:             clivalue: (params.sourmashgather_ignoreabn ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_prefetch': [
kkonganti@17:             clihelp: 'Use prefetch before gather. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_prefetch}",
kkonganti@17:             cliflag: '--prefetch',
kkonganti@17:             clivalue: (params.sourmashgather_prefetch ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_noprefetch': [
kkonganti@17:             clihelp: 'Do not use prefetch before gather. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_noprefetch}",
kkonganti@17:             cliflag: '--no-prefetch',
kkonganti@17:             clivalue: (params.sourmashgather_noprefetch ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_ani_ci': [
kkonganti@17:             clihelp: 'Output confidence intervals for ANI estimates. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_ani_ci}",
kkonganti@17:             cliflag: '--estimate-ani-ci',
kkonganti@17:             clivalue: (params.sourmashgather_ani_ci ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_k': [
kkonganti@17:             clihelp: 'The k-mer size to select. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_k}",
kkonganti@17:             cliflag: '-k',
kkonganti@17:             clivalue: (params.sourmashgather_k ?: '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_protein': [
kkonganti@17:             clihelp: 'Choose a protein signature. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_protein}",
kkonganti@17:             cliflag: '--protein',
kkonganti@17:             clivalue: (params.sourmashgather_protein ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_noprotein': [
kkonganti@17:             clihelp: 'Do not choose a protein signature. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_noprotein}",
kkonganti@17:             cliflag: '--no-protein',
kkonganti@17:             clivalue: (params.sourmashgather_noprotein ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_dayhoff': [
kkonganti@17:             clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_dayhoff}",
kkonganti@17:             cliflag: '--dayhoff',
kkonganti@17:             clivalue: (params.sourmashgather_dayhoff ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_nodayhoff': [
kkonganti@17:             clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_nodayhoff}",
kkonganti@17:             cliflag: '--no-dayhoff',
kkonganti@17:             clivalue: (params.sourmashgather_nodayhoff ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_hp': [
kkonganti@17:             clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_hp}",
kkonganti@17:             cliflag: '--hp',
kkonganti@17:             clivalue: (params.sourmashgather_hp ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_nohp': [
kkonganti@17:             clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_nohp}",
kkonganti@17:             cliflag: '--no-hp',
kkonganti@17:             clivalue: (params.sourmashgather_nohp ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_dna': [
kkonganti@17:             clihelp: 'Choose DNA signature. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_dna}",
kkonganti@17:             cliflag: '--dna',
kkonganti@17:             clivalue: (params.sourmashgather_dna ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_nodna': [
kkonganti@17:             clihelp: 'Do not choose DNA signature. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_nodna}",
kkonganti@17:             cliflag: '--no-dna',
kkonganti@17:             clivalue: (params.sourmashgather_nodna ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_scaled': [
kkonganti@17:             clihelp: 'Scaled value should be between 100 and 1e6. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_scaled}",
kkonganti@17:             cliflag: '--scaled',
kkonganti@17:             clivalue: (params.sourmashgather_scaled ?: '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_inc_pat': [
kkonganti@17:             clihelp: 'Search only signatures that match this pattern in name, filename, or md5. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_inc_pat}",
kkonganti@17:             cliflag: '--include-db-pattern',
kkonganti@17:             clivalue: (params.sourmashgather_inc_pat ?: '')
kkonganti@17:         ],
kkonganti@17:         'sourmashgather_exc_pat': [
kkonganti@17:             clihelp: 'Search only signatures that do not match this pattern in name, filename, or md5. ' +
kkonganti@17:                 "Default: ${params.sourmashgather_exc_pat}",
kkonganti@17:             cliflag: '--exclude-db-pattern',
kkonganti@17:             clivalue: (params.sourmashgather_exc_pat ?: '')
kkonganti@17:         ]
kkonganti@17:     ]
kkonganti@17: 
kkonganti@17:     toolspecs.each {
kkonganti@17:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     return tool
kkonganti@17: }