kkonganti@1: // Help text for sourmash search within CPIPES.
kkonganti@1: 
kkonganti@1: def sourmashsearchHelp(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:         'sourmashsearch_run': [
kkonganti@1:             clihelp: 'Run `sourmash search` tool. Default: ' +
kkonganti@1:                 (params.sourmashsearch_run ?: false),
kkonganti@1:             cliflag: null,
kkonganti@1:             clivalue: null
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_n': [
kkonganti@1:             clihelp: 'Number of results to report. ' +
kkonganti@1:                 'By default, will terminate at --sourmashsearch_thr value. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_n}",
kkonganti@1:             cliflag: '-n',
kkonganti@1:             clivalue: (params.sourmashsearch_n ?: '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_thr': [
kkonganti@1:             clihelp: 'Reporting threshold (similarity) to return results. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_thr}",
kkonganti@1:             cliflag: '--threshold',
kkonganti@1:             clivalue: (params.sourmashsearch_thr ?: '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_contain': [
kkonganti@1:             clihelp: 'Score based on containment rather than similarity. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_contain}",
kkonganti@1:             cliflag: '--containment',
kkonganti@1:             clivalue: (params.sourmashsearch_contain ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_maxcontain': [
kkonganti@1:             clihelp: 'Score based on max containment rather than similarity. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_contain}",
kkonganti@1:             cliflag: '--max-containment',
kkonganti@1:             clivalue: (params.sourmashsearch_maxcontain ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_ignoreabn': [
kkonganti@1:             clihelp: 'Do NOT use k-mer abundances if present. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_ignoreabn}",
kkonganti@1:             cliflag: '--ignore-abundance',
kkonganti@1:             clivalue: (params.sourmashsearch_ignoreabn ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_ani_ci': [
kkonganti@1:             clihelp: 'Output confidence intervals for ANI estimates. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_ani_ci}",
kkonganti@1:             cliflag: '--estimate-ani-ci',
kkonganti@1:             clivalue: (params.sourmashsearch_ani_ci ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_k': [
kkonganti@1:             clihelp: 'The k-mer size to select. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_k}",
kkonganti@1:             cliflag: '-k',
kkonganti@1:             clivalue: (params.sourmashsearch_k ?: '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_protein': [
kkonganti@1:             clihelp: 'Choose a protein signature. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_protein}",
kkonganti@1:             cliflag: '--protein',
kkonganti@1:             clivalue: (params.sourmashsearch_protein ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_noprotein': [
kkonganti@1:             clihelp: 'Do not choose a protein signature. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_noprotein}",
kkonganti@1:             cliflag: '--no-protein',
kkonganti@1:             clivalue: (params.sourmashsearch_noprotein ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_dayhoff': [
kkonganti@1:             clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_dayhoff}",
kkonganti@1:             cliflag: '--dayhoff',
kkonganti@1:             clivalue: (params.sourmashsearch_dayhoff ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_nodayhoff': [
kkonganti@1:             clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_nodayhoff}",
kkonganti@1:             cliflag: '--no-dayhoff',
kkonganti@1:             clivalue: (params.sourmashsearch_nodayhoff ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_hp': [
kkonganti@1:             clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_hp}",
kkonganti@1:             cliflag: '--hp',
kkonganti@1:             clivalue: (params.sourmashsearch_hp ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_nohp': [
kkonganti@1:             clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_nohp}",
kkonganti@1:             cliflag: '--no-hp',
kkonganti@1:             clivalue: (params.sourmashsearch_nohp ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_dna': [
kkonganti@1:             clihelp: 'Choose DNA signature. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_dna}",
kkonganti@1:             cliflag: '--dna',
kkonganti@1:             clivalue: (params.sourmashsearch_dna ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_nodna': [
kkonganti@1:             clihelp: 'Do not choose DNA signature. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_nodna}",
kkonganti@1:             cliflag: '--no-dna',
kkonganti@1:             clivalue: (params.sourmashsearch_nodna ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_scaled': [
kkonganti@1:             clihelp: 'Scaled value should be between 100 and 1e6. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_scaled}",
kkonganti@1:             cliflag: '--scaled',
kkonganti@1:             clivalue: (params.sourmashsearch_scaled ?: '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_inc_pat': [
kkonganti@1:             clihelp: 'Search only signatures that match this pattern in name, filename, or md5. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_inc_pat}",
kkonganti@1:             cliflag: '--include-db-pattern',
kkonganti@1:             clivalue: (params.sourmashsearch_inc_pat ?: '')
kkonganti@1:         ],
kkonganti@1:         'sourmashsearch_exc_pat': [
kkonganti@1:             clihelp: 'Search only signatures that do not match this pattern in name, filename, or md5. ' +
kkonganti@1:                 "Default: ${params.sourmashsearch_exc_pat}",
kkonganti@1:             cliflag: '--exclude-db-pattern',
kkonganti@1:             clivalue: (params.sourmashsearch_exc_pat ?: '')
kkonganti@1:         ]
kkonganti@1:     ]
kkonganti@1: 
kkonganti@1:     toolspecs.each {
kkonganti@1:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@1:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     return tool
kkonganti@1: }