cwlVersion: v1.0
class: Workflow
inputs:
  muscle_infile: File
  diags_flag: boolean
  substitutionmodel: string

outputs:
  output:
    type: File
    outputBinding: raxml.output

steps:
  run_muscle:
    class: CommandLineTool
    baseCommand: muscle
    inputs:
      muscle_infile:
        type: File
        inputBinding:
          prefix: -in
          separate: true
          position: 1
      diags_flag:
        type: boolean
        inputBinding:
          position: 2
          prefix: -diags
    outputs:
      muscle_outfile:
        type: File
        outputBinding:
          glob: muscle_out.fasta

  run_raxml:
    run:
      class: CommandLineTool
      baseCommand: raxmlHPC
      inputs:
        raxml_infile:
          type: File
          inputBinding:
            prefix: -s
            separate: true
            position: 1
            glob: muscle_out.fasta
        substitutionmodel:
          type: string
          inputBinding:
            prefix: -m
            separate: true
            position: 2
      outputs:
        raxml_output:
          type: File
          outputBinding:
            prefix: -n
            separate: true
            glob: raxml_output