cwlVersion: v1.2

label: "Prepare Unannotated Sequences"

doc: "Prepare Unannotated Sequences"

class: CommandLineTool

baseCommand: bacterial_prepare_unannotated

arguments: [ -submission-mode-genbank, -nogenbank ]

inputs:

asn_cache:

type: Directory

inputBinding:

prefix: -asn-cache

gc_assembly:

type: File

inputBinding:

prefix: -gc-assembly

ids:

type: File

inputBinding:

prefix: -ids

submit_block:

type: File

inputBinding:

prefix: -submit-block

taxon_db:

type: File

inputBinding:

prefix: -taxon-db

no_internet:

type: boolean?

inputBinding:

prefix: -no-internet

master_desc_name:

type: string?

default: master-desc.asn

inputBinding:

prefix: -master-desc

sequences_name:

type: string?

default: sequences.asn

inputBinding:

prefix: -o

plasmids_name:

type: string?

default: plasmids.seqids

inputBinding:

prefix: -plasmids

outputs:

master_desc:

type: File

outputBinding:

glob: $(inputs.master_desc_name)

sequences:

type: File

outputBinding:

glob: $(inputs.sequences_name)

plasmids:

type: File

outputBinding:

glob: $(inputs.plasmids_name)