kkonganti@11: // Help text for sourmash sigkmers within CPIPES.
kkonganti@11: 
kkonganti@11: def sourmashsigkmersHelp(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:         'sourmashsigkmers_run': [
kkonganti@11:             clihelp: 'Run `sourmash sigkmers` tool. Default: ' +
kkonganti@11:                 (params.sourmashsigkmers_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_k': [
kkonganti@11:             clihelp: 'The k-mer size to select. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_k}",
kkonganti@11:             cliflag: '-k',
kkonganti@11:             clivalue: (params.sourmashsigkmers_k ?: '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_protein': [
kkonganti@11:             clihelp: 'Choose a protein signature. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_protein}",
kkonganti@11:             cliflag: '--protein',
kkonganti@11:             clivalue: (params.sourmashsigkmers_protein ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_noprotein': [
kkonganti@11:             clihelp: 'Do not choose a protein signature. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_noprotein}",
kkonganti@11:             cliflag: '--no-protein',
kkonganti@11:             clivalue: (params.sourmashsigkmers_noprotein ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_dayhoff': [
kkonganti@11:             clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_dayhoff}",
kkonganti@11:             cliflag: '--dayhoff',
kkonganti@11:             clivalue: (params.sourmashsigkmers_dayhoff ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_nodayhoff': [
kkonganti@11:             clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_nodayhoff}",
kkonganti@11:             cliflag: '--no-dayhoff',
kkonganti@11:             clivalue: (params.sourmashsigkmers_nodayhoff ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_hp': [
kkonganti@11:             clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_hp}",
kkonganti@11:             cliflag: '--hp',
kkonganti@11:             clivalue: (params.sourmashsigkmers_hp ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_nohp': [
kkonganti@11:             clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_nohp}",
kkonganti@11:             cliflag: '--no-hp',
kkonganti@11:             clivalue: (params.sourmashsigkmers_nohp ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_dna': [
kkonganti@11:             clihelp: 'Choose DNA signature. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_dna}",
kkonganti@11:             cliflag: '--dna',
kkonganti@11:             clivalue: (params.sourmashsigkmers_dna ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_nodna': [
kkonganti@11:             clihelp: 'Do not choose DNA signature. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_nodna}",
kkonganti@11:             cliflag: '--no-dna',
kkonganti@11:             clivalue: (params.sourmashsigkmers_nodna ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_save_kmers': [
kkonganti@11:             clihelp: 'Save k-mers and hash values to a CSV file. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_save_kmers}",
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_save_seqs': [
kkonganti@11:             clihelp: 'Save sequences with matching hash values to a FASTA file. ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_save_seqs}",
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'sourmashsigkmers_translate': [
kkonganti@11:             clihelp: 'Translate DNA k-mers into amino acids (for protein, dayhoff, and hp sketches). ' +
kkonganti@11:                 "Default: ${params.sourmashsigkmers_translate}",
kkonganti@11:             cliflag: '--translate',
kkonganti@11:             clivalue: (params.sourmashsigkmers_translate ? ' ' : '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }