name: clonalframeml
description: Predict recomination events in bacterial genomes
keywords:
  - fasta
  - multiple sequence alignment
  - recombination
tools:
  - clonalframeml:
      description: Efficient inferencing of recombination in bacterial genomes
      homepage: https://github.com/xavierdidelot/ClonalFrameML
      documentation: https://github.com/xavierdidelot/clonalframeml/wiki
      tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML
      doi: "10.1371/journal.pcbi.1004041"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - msa:
      type: file
      description: A multiple seqeunce alignmnet in FASTA format
      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
  - newick:
      type: file
      description: A Newick formated tree based on multiple sequence alignment
      pattern: "*.{newick,treefile,dnd}"

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"
  - emsim:
      type: file
      description: Bootstrapped values for the three parameters R/theta, nu and delta
      pattern: "*.emsim.txt"
  - em:
      type: file
      description: Point estimates for R/theta, nu, delta and the branch lengths
      pattern: "*.em.txt"
  - fasta:
      type: file
      description: Sequence reconstructed by maximum likelihood
      pattern: "*.ML_sequence.fasta"
  - newick:
      type: file
      description: Tree with all nodes labelled
      pattern: "*.labelled_tree.newick"
  - pos_ref:
      type: file
      description: CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta
      pattern: "*.position_cross_reference.txt"
  - status:
      type: file
      description: List of reconstructed recombination events
      pattern: "*.importation_status.txt"

authors:
  - "@rpetit3"