name: dastool_scaffolds2bin
description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
keywords:
  - binning
  - das tool
  - table
  - de novo
  - bins
  - contigs
  - assembly
  - das_tool
tools:
  - dastool:
      description: |
        DAS Tool is an automated method that integrates the results
        of a flexible number of binning algorithms to calculate an optimized, non-redundant
        set of bins from a single assembly.

      homepage: https://github.com/cmks/DAS_Tool
      documentation: https://github.com/cmks/DAS_Tool
      tool_dev_url: https://github.com/cmks/DAS_Tool
      doi: "10.1038/s41564-018-0171-1"
      licence: ["BSD"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins
      pattern: "*.{fa,fas,fasta}"
  - binner:
      type: val
      description: Name of the binning software (optional)
  - extension:
      type: val
      description: Fasta file extension (fa | fas | fasta | ...)

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"
  - scaffolds2bin:
      type: file
      description: tabular scaffolds2bin file for DAS tool input
      pattern: "*.scaffolds2bin.tsv"

authors:
  - "@maxibor"