name: bamtools_convert
description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
keywords:
  - bamtools
  - bamtools/convert
  - bam
  - convert
  - bed
  - fasta
  - fastq
  - json
  - pileup
  - sam
  - yaml
tools:
  - bamtools:
      description: C++ API & command-line toolkit for working with BAM data
      homepage: http://github.com/pezmaster31/bamtools
      documentation: https://github.com/pezmaster31/bamtools/wiki
      tool_dev_url: http://github.com/pezmaster31/bamtools

      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM file
      pattern: "*.bam"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - out:
      type: file
      description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
      pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}"

authors:
  - "@sguizard"
