class: GalaxyWorkflow
inputs:
  reference:
    type: data
    format:
      - fasta
      - bwa_mem2_index
outputs:
  output:
    outputSource: use_index/output
steps:
  create_index:
    tool_id: create_directory_index
    when: $(inputs.reference.format != "bwa_mem2_index" )
    in:
      reference:
        source: reference
  pick_value:
    tool_id: pick_value
    in:
      style_cond|type_cond|pick_from_0|value:
        source: create_index/index
      style_cond|type_cond|pick_from_1|value:
        source: reference
    tool_state:
      style_cond:
        pick_style: first
        type_cond:
          param_type: data
          pick_from:
          - value: create_index/index
          - value: reference
  use_index:
    tool_id: use_directory_index
    in:
      reference: pick_value/data_param