_prokka

#compdef prokka

#prokka [options] <contigs.fasta>

_prokka () {
	local ret=1
	local -a args
	args+=(
		# General:
		'(- *)--citation[Print citation for referencing Prokka]'
		'(- *)--docs[Show full manual/documentation]'
		'(- *)--help[This help]'
		'(- *)--version[Print version and exit]'
		'--debug[Debug mode: keep all temporary files]'
		'--quiet[No screen output]'
		# Setup:
		'--cleandb[Remove all database indices]'
		'--depends[List all software dependencies]'
		'--listdb[List all configured databases]'
		'--setupdb[Index all installed databases]'
		# Outputs:
		'--accver=[Version to put in Genbank file (default 1)]: :'
		'--addgenes[Add gene features for each CDS feature]'
		'--addmrna[Add mRNA features for each CDS feature]'
		'--centre=[Sequencing centre ID. (default '')]: :'
		'--compliant[Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX]'
		'--force[Force overwriting existing output folder]'
		'--gffver=[GFF version (default 3)]: :(1 2 3)'
		'--increment=[Locus tag counter increment (default 1)]: :'
		'--locustag=[Locus tag prefix]: :'
		'--outdir=[Output folder]:dir:_files -/'
		'--prefix=[Filename output prefix]: :'
		# Organism details:
		'--genus=[Genus name (default: Genus)]:string:'
		'--plasmid=[Plasmid name or identifier]:string:'
		'--species=[Species name (default: species)]:string:'
		'--strain=[Strain name (default: strain)]:string:'
		# Annotations:
		'--cdsrnaolap[Allow RNA to overlap CDS]'
		'--gcode=[Genetic code / Translation table (set if --kingdom is set)]: :'
		'--gram=[Gram: -/neg +/pos]: :(+ - pos neg)'
		'--hmms=[Trusted HMM to first annotate from]: :'
		'--kingdom=[Annotation mode (default Bacteria)]: :(Archaea  Bacteria  Mitochondria  Viruses)'
		'--metagenome[Improve gene predictions for highly fragmented genomes]'
		'--proteins=[FASTA or GBK file to use as 1st priority]:file:_files'
		'--rawproduct[Do not clean up /product annotation]'
		'--usegenus[Use genus-specific BLAST databases (needs --genus)]'
		# Computation:
		'--cpus=[Number of CPUs to use (default 8, 0=all)]:int:'
		'--evalue=[Similarity e-value cut-off (default 1e-06)]:float:'
		'--fast[Fast mode - only use basic BLASTP databases]'
		'--mincontiglen=[Minimum contig size (NCBI needs 200, default 1)]:int:'
		'--noanno[For CDS just set /product="unannotated protein"]'
		'--norrna[Do not run rRNA search]'
		'--notrna[Do not run tRNA search]'
		'--rfam[Enable searching for ncRNAs with Infernal+Rfam (SLOW!)]'
		'--rnammer[Prefer RNAmmer over Barrnap for rRNA prediction]'
	)

	_arguments $args[@] '*:file:_files' && ret=0
	return 0
}

_prokka