pepr_callpeak.yaml 2.52 KB
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pepr_callpeak:
  inputs:
    - name: control
      type: file
      file_type: bed
    - name: signal
      type: file
      file_type: bed
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    - name: prefix
      type: string
    - name: peak_type
      type: string
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  additional_inputs: null
  outputs:
    - name: pepr_result
      type: file
      file_type: bed
    - name: pepr_parameters
      type: file
      file_type: txt
  command: pepr
  arguments:
    - "-c":
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        type: list
        separator: ","
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        changeable: false
        required: true
        has_value: true
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        default:
          - $inputs.0
          - $inputs.0
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    - "-i":
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        type: list
        separator: ","
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        changeable: false
        required: true
        has_value: true
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        default:
          - $inputs.1
          - $inputs.1
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    - "-n":
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        type: file
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        changeable: true
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        required: true
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        has_value: true
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        default: $inputs.2
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    - "-f":
        type: string
        changeable: true
        required: true
        has_value: true
        default: "bed"
    - "-s":
        type: numeric
        changeable: true
        required: false
        has_value: true
        default: 10
    - "-w":
        type: numeric
        changeable: true
        required: false
        has_value: true
        default: 100
    - "--diff":
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        type: string
        changeable: false
        required: true
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        has_value: false
    - "--threshold":
        type: string
        changeable: true
        required: false
        has_value: true
        default: "1e-5"
    - "--peaktype":
        type: string
        changeable: true
        required: true
        has_value: true
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        default: "$inputs.3"
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    - "--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
        default: 10000000
    - "--num-processors":
        type: numeric
        changeable: true
        required: false
        has_value: true
        default: 1
    - "--input-directory":
        type: string
        changeable: true
        required: false
        has_value: true
        default: ""
    - "--output-directory":
        type: string
        changeable: true
        required: false
        has_value: true
        default: ""
    - "--verbose":
        type: string
        changeable: false
        required: true
        has_value: false
  walltime: 120
  memory: 16000
  cores: 1
  nodes: 1