name: ncbigenomedownload
description: A tool to quickly download assemblies from NCBI's Assembly database
keywords:
  - fasta
  - download
  - assembly
tools:
  - ncbigenomedownload:
      description: Download genome files from the NCBI FTP server.
      homepage: https://github.com/kblin/ncbi-genome-download
      documentation: https://github.com/kblin/ncbi-genome-download
      tool_dev_url: https://github.com/kblin/ncbi-genome-download
      licence: ["Apache Software License"]
      identifier: ""
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - accessions:
      type: file
      description: List of accessions (one per line) to download
      pattern: "*.txt"
      ontologies: []
  - taxids:
      type: file
      description: List of taxids (one per line) to download
      pattern: "*.txt"
      ontologies: []
  - groups:
      type: string
      description: NCBI taxonomic groups to download. Can be a comma-separated list.
        Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes',
        'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral']
output:
  gbk:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_genomic.gbff.gz":
          type: file
          description: GenBank format of the genomic sequence(s) in the assembly
          pattern: "*_genomic.gbff.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  fna:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_genomic.fna.gz":
          type: file
          description: FASTA format of the genomic sequence(s) in the assembly.
          pattern: "*_genomic.fna.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  rm:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_rm.out.gz":
          type: file
          description: RepeatMasker output for eukaryotes.
          pattern: "*_rm.out.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  features:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_feature_table.txt.gz":
          type: file
          description: Tab-delimited text file reporting locations and attributes for
            a subset of annotated features
          pattern: "*_feature_table.txt.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  gff:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_genomic.gff.gz":
          type: file
          description: Annotation of the genomic sequence(s) in GFF3 format
          pattern: "*_genomic.gff.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  faa:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_protein.faa.gz":
          type: file
          description: FASTA format of the accessioned protein products annotated on
            the genome assembly.
          pattern: "*_protein.faa.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  gpff:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_protein.gpff.gz":
          type: file
          description: GenPept format of the accessioned protein products annotated
            on the genome assembly.
          pattern: "*_protein.gpff.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  wgs_gbk:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_wgsmaster.gbff.gz":
          type: file
          description: GenBank flat file format of the WGS master for the assembly
          pattern: "*_wgsmaster.gbff.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  cds:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_cds_from_genomic.fna.gz":
          type: file
          description: FASTA format of the nucleotide sequences corresponding to all
            CDS features annotated on the assembly
          pattern: "*_cds_from_genomic.fna.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  rna:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_rna.fna.gz":
          type: file
          description: FASTA format of accessioned RNA products annotated on the genome
            assembly
          pattern: "*_rna.fna.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  rna_fna:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_rna_from_genomic.fna.gz":
          type: file
          description: FASTA format of the nucleotide sequences corresponding to all
            RNA features annotated on the assembly
          pattern: "*_rna_from_genomic.fna.gz"
          ontologies:
            - edam: http://edamontology.org/format_3989 # GZIP format
  report:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_assembly_report.txt":
          type: file
          description: Tab-delimited text file reporting the name, role and sequence
            accession.version for objects in the assembly
          pattern: "*_assembly_report.txt"
          ontologies: []
  stats:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_assembly_stats.txt":
          type: file
          description: Tab-delimited text file reporting statistics for the assembly
          pattern: "*_assembly_stats.txt"
          ontologies: []
  versions_ncbigenomedownload:
    - - ${task.process}:
          type: string
          description: The process name
      - ncbigenomedownload:
          type: string
          description: The tool name
      - ncbi-genome-download --version:
          type: eval
          description: The tool version
topics:
  versions:
    - - ${task.process}:
          type: string
          description: The process name
      - ncbigenomedownload:
          type: string
          description: The tool name
      - ncbi-genome-download --version:
          type: eval
          description: The tool version
authors:
  - "@rpetit3"
maintainers:
  - "@rpetit3"
