kkonganti@0: // Help text for shovill within CPIPES.
kkonganti@0: 
kkonganti@0: def shovillHelp(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:         'shovill_run': [
kkonganti@0:             clihelp: 'Run shovill tool. Default: ' +
kkonganti@0:                 (params.shovill_run ?: false),
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'shovill_depth': [
kkonganti@0:             clihelp: 'Sub-sample R1/R2 to this depth. Disable with --shovill_depth 0. ' +
kkonganti@0:                 "Default: ${params.shovill_depth}",
kkonganti@0:             cliflag: '--depth',
kkonganti@0:             clivalue: (params.shovill_depth ?: 150)
kkonganti@0:         ],
kkonganti@0:         'shovill_gsize': [
kkonganti@0:             clihelp: 'Estimated genome size eg. 3.2M. <false=AUTODETECT>. ' +
kkonganti@0:                 "Default: ${params.shovill_gsize}",
kkonganti@0:             cliflag: '--gsize',
kkonganti@0:             clivalue: (params.shovill_gsize ?: '')
kkonganti@0:         ],
kkonganti@0:         'shovill_minlen': [
kkonganti@0:             clihelp: 'Minimum contig length. <false=AUTO>. ' +
kkonganti@0:                 "Default: ${params.shovill_minlen}",
kkonganti@0:             cliflag: '--minlen',
kkonganti@0:             clivalue: (params.shovill_minlen ?: '')
kkonganti@0:         ],
kkonganti@0:         'shovill_mincov': [
kkonganti@0:             clihelp: "Minimum contig coverage. <false=AUTO>. " +
kkonganti@0:                 "Default: ${params.shovill_mincov}",
kkonganti@0:             cliflag: '--mincov',
kkonganti@0:             clivalue: (params.shovill_mincov ?: '')
kkonganti@0:         ],
kkonganti@0:         'shovill_namefmt': [
kkonganti@0:             clihelp: "Format of contig FASTA IDs in 'printf' style. " +
kkonganti@0:                 "Default: ${params.shovill_namefmt}",
kkonganti@0:             cliflag: '--namefmt',
kkonganti@0:             clivalue: (params.shovill_namefmt ?: '')
kkonganti@0:         ],
kkonganti@0:         'shovill_keepfiles': [
kkonganti@0:             clihelp: 'Keep intermediate files. ' +
kkonganti@0:                 "Default: ${params.shovill_keepfiles}",
kkonganti@0:             cliflag: '--keepfiles',
kkonganti@0:             clivalue: (params.shovill_keepfiles ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'shovill_assembler': [
kkonganti@0:             clihelp: 'Assembler: skesa, megahit, velvet, or spades. ' +
kkonganti@0:                 "Default: ${params.shovill_assembler}",
kkonganti@0:             cliflag: '--assembler',
kkonganti@0:             clivalue: (params.shovill_assembler ?: '')
kkonganti@0:         ],
kkonganti@0:         'shovill_opts': [
kkonganti@0:             clihelp: "Extra assembler options in quotes. Ex: '--sc'. " +
kkonganti@0:                 "Default: ${params.shovill_opts}",
kkonganti@0:             cliflag: '--opts',
kkonganti@0:             clivalue: (params.shovill_opts ?: '')
kkonganti@0:         ],
kkonganti@0:         'shovill_kmers': [
kkonganti@0:             clihelp: 'K-mers to use. <false=AUTO>. ' +
kkonganti@0:                 "Default: ${params.shovill_kmers}",
kkonganti@0:             cliflag: '--kmers',
kkonganti@0:             clivalue: (params.shovill_kmers ?: '')
kkonganti@0:         ],
kkonganti@0:         'shovill_trim': [
kkonganti@0:             clihelp: 'Enable adator trimming. ' +
kkonganti@0:                 "Default: ${params.shovill_trim}",
kkonganti@0:             cliflag: '--trim',
kkonganti@0:             clivalue: (params.shovill_trim ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'shovill_noreadcorr': [
kkonganti@0:             clihelp: 'Disable read error correction. ' +
kkonganti@0:                 "Default: ${params.shovill_noreadcorr}",
kkonganti@0:             cliflag: '--noreadcorr',
kkonganti@0:             clivalue: (params.shovill_noreadcorr ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'shovill_nostitch': [
kkonganti@0:             clihelp: 'Disable read stitching. ' +
kkonganti@0:                 "Default: ${params.shovill_nostitch}",
kkonganti@0:             cliflag: '--nostitch',
kkonganti@0:             clivalue: (params.shovill_nostitch ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'shovill_nocorr': [
kkonganti@0:             clihelp: 'Disable post-assembly correction. ' +
kkonganti@0:                 "Default: ${params.shovill_nocorr}",
kkonganti@0:             cliflag: '--nocorr',
kkonganti@0:             clivalue: (params.shovill_nocorr ? ' ' : '')
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }