kkonganti@0: // Help text for prokka within CPIPES.
kkonganti@0: 
kkonganti@0: def prokkaHelp(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:         'prokka_run': [
kkonganti@0:             clihelp: 'Run prokka tool. Default: ' +
kkonganti@0:                 (params.prokka_run ?: false),
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'prokka_dbdir': [
kkonganti@0:             clihelp: 'Path to prokka database root folder. ' +
kkonganti@0:                 "Default: ${params.prokka_dbdir}",
kkonganti@0:             cliflag: '--dbdir',
kkonganti@0:             clivalue: (params.prokka_dbdir ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_addgenes': [
kkonganti@0:             clihelp: "Add 'gene' features for each 'CDS' feature. " +
kkonganti@0:                 "Default: ${params.prokka_addgenes}",
kkonganti@0:             cliflag: '--addgenes',
kkonganti@0:             clivalue: (params.prokka_addgenes ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_addmrna': [
kkonganti@0:             clihelp: "Add 'mRNA' features for each 'CDS' feature. " +
kkonganti@0:                 "Default: ${params.prokka_addmrna}",
kkonganti@0:             cliflag: '--addmrna',
kkonganti@0:             clivalue: (params.prokka_addmrna ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_locustag': [
kkonganti@0:             clihelp: "Locus tag prefix. " +
kkonganti@0:                 "Default: ${params.prokka_locustag}",
kkonganti@0:             cliflag: '--locustag',
kkonganti@0:             clivalue: (params.prokka_locustag ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_increment': [
kkonganti@0:             clihelp: "Locus tag counter increment. " +
kkonganti@0:                 "Default: ${params.prokka_increment}",
kkonganti@0:             cliflag: '--increment',
kkonganti@0:             clivalue: (params.prokka_increment ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_gffver': [
kkonganti@0:             clihelp: 'GFF version. ' +
kkonganti@0:                 "Default: ${params.prokka_gffver}",
kkonganti@0:             cliflag: '-gffver',
kkonganti@0:             clivalue: (params.prokka_gffver ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_compliant': [
kkonganti@0:             clihelp: ' Force Genbank/ENA/DDJB compliance i.e. ' +
kkonganti@0:                 '--prokka_addgenes --prokka_mincontiglen 200 --prokka_centre XXX. ' +
kkonganti@0:                 "Default: ${params.prokka_compliant}",
kkonganti@0:             cliflag: '--compliant',
kkonganti@0:             clivalue: (params.prokka_compliant ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_centre': [
kkonganti@0:             clihelp: 'Sequencing centre ID. ' +
kkonganti@0:                 "Default: ${params.prokka_centre}",
kkonganti@0:             cliflag: '--centre',
kkonganti@0:             clivalue: (params.prokka_centre ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_accver': [
kkonganti@0:             clihelp: 'Version to put in GenBank file. ' +
kkonganti@0:                 "Default: ${params.prokka_accver}",
kkonganti@0:             cliflag: '--accver',
kkonganti@0:             clivalue: (params.prokka_accver ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_genus': [
kkonganti@0:             clihelp: 'Genus name. ' +
kkonganti@0:                 "Default: ${params.prokka_genus}",
kkonganti@0:             cliflag: '--genus',
kkonganti@0:             clivalue: (params.prokka_genus ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_species': [
kkonganti@0:             clihelp: 'Species name. ' +
kkonganti@0:                 "Default: ${params.prokka_species}",
kkonganti@0:             cliflag: '--species',
kkonganti@0:             clivalue: (params.prokka_species ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_strain': [
kkonganti@0:             clihelp: 'Strain name. ' +
kkonganti@0:                 "Default: ${params.prokka_strain}",
kkonganti@0:             cliflag: '--strain',
kkonganti@0:             clivalue: (params.prokka_strain ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_plasmid': [
kkonganti@0:             clihelp: 'Plasmid name or identifier. ' +
kkonganti@0:                 "Default: ${params.prokka_plasmid}",
kkonganti@0:             cliflag: '--plasmid',
kkonganti@0:             clivalue: (params.prokka_plasmid ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_kingdom': [
kkonganti@0:             clihelp: 'Annotation mode: Archaea|Bacteria|Mitochondria|Viruses. ' +
kkonganti@0:                 "Default: ${params.prokka_kingdom}",
kkonganti@0:             cliflag: '--kingdom',
kkonganti@0:             clivalue: (params.prokka_kingdom ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_gcode': [
kkonganti@0:             clihelp: 'Genetic code / Translation table (set if --prokka_kingdom is set). ' +
kkonganti@0:                 "Default: ${params.prokka_gcode}",
kkonganti@0:             cliflag: '--gcode',
kkonganti@0:             clivalue: (params.prokka_gcode ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_usegenus': [
kkonganti@0:             clihelp: 'Use genus-specific BLAST databases (needs --prokka_genus) ' +
kkonganti@0:                 "Default: ${params.prokka_usegenus}",
kkonganti@0:             cliflag: '--usegenus',
kkonganti@0:             clivalue: (params.prokka_usegenus ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_metagenome': [
kkonganti@0:             clihelp: 'Improve gene predictions for highly fragmented genomes. ' +
kkonganti@0:                 "Default: ${params.prokka_metagenome}",
kkonganti@0:             cliflag: '--metagenome',
kkonganti@0:             clivalue: (params.prokka_metagenome ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_rawproduct': [
kkonganti@0:             clihelp: 'Version to put in GenBank file. ' +
kkonganti@0:                 "Default: ${params.prokka_rawproduct}",
kkonganti@0:             cliflag: '--rawproduct',
kkonganti@0:             clivalue: (params.prokka_rawproduct ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_cdsrnaolap': [
kkonganti@0:             clihelp: 'Do not clean up /product annotation. ' +
kkonganti@0:                 "Default: ${params.prokka_cdsrnaolap}",
kkonganti@0:             cliflag: '--cdsrnaolap',
kkonganti@0:             clivalue: (params.prokka_cdsrnaolap ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_evalue': [
kkonganti@0:             clihelp: 'Similarity e-value cut-off. ' +
kkonganti@0:                 "Default: ${params.prokka_evalue}",
kkonganti@0:             cliflag: '--evalue',
kkonganti@0:             clivalue: (params.prokka_evalue ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_coverage': [
kkonganti@0:             clihelp: 'Minimum coverage on query protein. ' +
kkonganti@0:                 "Default: ${params.prokka_coverage}",
kkonganti@0:             cliflag: '--coverage',
kkonganti@0:             clivalue: (params.prokka_coverage ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_fast': [
kkonganti@0:             clihelp: 'Fast mode - only use basic BLASTP databases. ' +
kkonganti@0:                 "Default: ${params.prokka_fast}",
kkonganti@0:             cliflag: '--fast',
kkonganti@0:             clivalue: (params.prokka_fast ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_noanno': [
kkonganti@0:             clihelp: 'For CDS just set /product="unannotated protein". ' +
kkonganti@0:                 "Default: ${params.prokka_noanno}",
kkonganti@0:             cliflag: '--noanno',
kkonganti@0:             clivalue: (params.prokka_noanno ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_mincontiglen': [
kkonganti@0:             clihelp: 'Minimum contig size [NCBI needs 200]. ' +
kkonganti@0:                 "Default: ${params.prokka_mincontiglen}",
kkonganti@0:             cliflag: '--mincontiglen',
kkonganti@0:             clivalue: (params.prokka_mincontiglen ?: '')
kkonganti@0:         ],
kkonganti@0:         'prokka_rfam': [
kkonganti@0:             clihelp: 'Enable searching for ncRNAs with Infernal+Rfam (SLOW!). ' +
kkonganti@0:                 "Default: ${params.prokka_rfam}",
kkonganti@0:             cliflag: '--rfam',
kkonganti@0:             clivalue: (params.prokka_rfam ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_norrna': [
kkonganti@0:             clihelp: "Don't run rRNA search. " +
kkonganti@0:                 "Default: ${params.prokka_norrna}",
kkonganti@0:             cliflag: '--norrna',
kkonganti@0:             clivalue: (params.prokka_norrna ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_notrna': [
kkonganti@0:             clihelp: "Don't run tRNA search. " +
kkonganti@0:                 "Default: ${params.prokka_notrna}",
kkonganti@0:             cliflag: '--notrna',
kkonganti@0:             clivalue: (params.prokka_notrna ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prokka_rnammer': [
kkonganti@0:             clihelp: 'Prefer RNAmmer over Barrnap for rRNA prediction. ' +
kkonganti@0:                 "Default: ${params.prokka_rnammer}",
kkonganti@0:             cliflag: '--rnammer',
kkonganti@0:             clivalue: (params.prokka_rnammer ? ' ' : '')
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }