name: "pretextmap"
description: converts sam/bam/cram/pairs into genome contact map
keywords:
  - contact
  - bam
  - map
tools:
  - "pretextmap":
      description: "Paired REad TEXTure Mapper. Converts SAM formatted read pairs into
        genome contact maps."
      homepage: "https://github.com/wtsi-hpag/PretextMap"
      documentation: "https://github.com/wtsi-hpag/PretextMap/blob/master/README.md"
      licence: ["MIT"]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - input:
        type: file
        description: BAM/CRAM/SAM file or pairs formatted reads file
        pattern: "*.{bam,cram,sam,pairs.gz}"
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: Reference sequence file
        pattern: "*.{fasta,fna,fa}"
    - fai:
        type: file
        description: Reference sequence index file
        pattern: "*.{fai}"
output:
  - pretext:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.pretext":
          type: file
          description: pretext map
          pattern: "*.pretext"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@marrip"
  - "@getrudeln"
maintainers:
  - "@marrip"
  - "@getrudeln"
