pepr_callpeak.yaml 2.46 KB
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pepr_callpeak:
  inputs:
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    control.bed:
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      type: file
      file_type: bed
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    signal.bed:
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      type: file
      file_type: bed
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    prefix:
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      type: string
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    peak_type:
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      type: string
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  outputs:
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    result_peaks:
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      type: file
      file_type: bed
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    pepr_params:
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      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:
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          - $control.bed
          - $control.bed
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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:
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          - $signal.bed
          - $signal.bed
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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: $prefix
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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: $peak_type
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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