pepr_callpeak:
  inputs:
    control.bed:
      type: file
      file_type: bed
    signal.bed:
      type: file
      file_type: bed
    prefix:
      type: string
    peak_type:
      type: string
  outputs:
    result_peaks:
      type: file
      file_type: bed
    pepr_params:
      type: file
      file_type: txt
  command: PePr
  arguments:
    - "-c":
        type: file_list
        separator: ","
        changeable: false
        required: true
        has_value: true
        default:
          - $control.bed
          - $control.bed
    - "-i":
        type: file_list
        separator: ","
        changeable: false
        required: true
        has_value: true
        default:
          - $signal.bed
          - $signal.bed
    - "-n":
        type: string
        changeable: true
        required: true
        has_value: true
        default: $prefix
    - "-f":
        type: string
        changeable: true
        required: true
        has_value: true
        default: "bed"
    - "-s":
        type: numeric
        changeable: true
        required: false
        has_value: true
    - "-w":
        type: numeric
        changeable: true
        required: false
        has_value: true
    - "--threshold":
        type: string
        changeable: true
        required: false
        has_value: true
        default: "1e-5"
    - "--peaktype":
        type: string
        changeable: true
        required: true
        has_value: true
        default: $peak_type
    - "--normalization":
        type: string
        changeable: true
        required: false
        has_value: true
        default: "intra-group"
    - "--keep-max-dup":
        type: numeric
        changeable: true
        required: false
        has_value: true
    - "--num-processors":
        type: numeric
        changeable: true
        required: false
        has_value: true
        default: 1
  walltime: 120
  memory: 16000
  cores: 1
  nodes: 1