envnet_gnps2/workflowinput.yaml at main · biorack/envnet_gnps2 · GitHub

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workflowname: ENVnet_Workflow
workflowdescription: ENVnet_Workflow
workflowlongdescription: Compare Dissolved Organic Matter (DOM) Samples From Two Groups Using ENVnet
workflowversion: "1.1"
workflowfile: nf_workflow.nf
workflowautohide: false
adminonly: false
#This maps the parameters from an input form to those that will appear in nextflow
parameterlist:
    - displayname: File Selection
      paramtype: section

    - displayname: Group 1 (Control) Data Folder
      paramtype: fileselector
      nf_paramname: inputfiles1
      formplaceholder: Enter the path to data
      formvalue: ""
      targettaskfolder: inputfiles1
      optional: false
      selectsinglefile: false
      folderunroll: true

    - displayname: Group 2 (Treatment) Data Folder
      paramtype: fileselector
      nf_paramname: inputfiles2
      formplaceholder: Enter the path to data
      formvalue: ""
      targettaskfolder: inputfiles2
      optional: false
      selectsinglefile: false
      folderunroll: true

    - displayname: General Parameters
      paramtype: section

    - displayname: Group 1 (Control) Name
      paramtype: text
      nf_paramname: inputfiles1_name
      formplaceholder: Enter data group 1 name.
      formvalue: ""
      optional: false

    - displayname: Group 2 (Treatment) Name
      paramtype: text
      nf_paramname: inputfiles2_name
      formplaceholder: Enter data group 2 name.
      formvalue: ""
      optional: false

    - displayname: Normalize Intensities (By Total Intensity)
      paramtype: select
      nf_paramname: normalize_ints
      formvalue: "0"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"

    - displayname: Require MS/MS Support For Statistical Analysis
      paramtype: select
      nf_paramname: require_ms2_support
      formvalue: "0"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"

    - displayname: Peak Intensity Value
      paramtype: select
      nf_paramname: peak_value
      formvalue: "peak_area"
      options:
        - value: "peak_area"
          display: "Peak Area"
        - value: "peak_height"
          display: "Peak Height"

    - displayname: Analysis Parameters
      paramtype: section

    - displayname: m/z Tolerance (ppm)
      paramtype: text
      nf_paramname: mz_tolerance
      formplaceholder: Enter the mz_tolerance. Used for MS1 and precursor m/z comparisons
      formvalue: "10"
      optional: true

    - displayname: Minimum Retention Time (Minutes)
      paramtype: text
      nf_paramname: rt_min
      formplaceholder: Enter the rt_min. Used to filter features from data files outside of range
      formvalue: "1"
      optional: true

    - displayname: Maximum Retention Time (Minutes)
      paramtype: text
      nf_paramname: rt_max
      formplaceholder: Enter the rt_max. Used to filter features from data files outside of range
      formvalue: "9"
      optional: true

    - displayname: Minimum Number of Data Points
      paramtype: text
      nf_paramname: num_data_min
      formplaceholder: Enter the num_data_min. Used to filter features from data files lower than min. A data point is defined as the detection of a particular m/z in one scan.
      formvalue: "5"
      optional: true

    - displayname: Minimum MS/MS Score
      paramtype: text
      nf_paramname: msms_score_min
      formplaceholder: Enter the msms_score_min.
      formvalue: "0.5"
      optional: true

    - displayname: Minimum MS/MS Matching Ion Counts
      paramtype: text
      nf_paramname: msms_matches_min
      formplaceholder: Enter the msms_matches_min.
      formvalue: "3"
      optional: true

    # Removed for now, can be added back later
    # - displayname: Cosmograph Visualization Parameters
    #   paramtype: section

    # - displayname: Log2 Fold Change Color Scale Max
    #   paramtype: text
    #   nf_paramname: max_log_change
    #   formplaceholder: Enter the max_log_change. Used for visualization in cosmograph, doesn't override actual values.
    #   formvalue: "1"
    #   optional: true

    # - displayname: Compound Class & Set Cover Analysis Parameters
    #   paramtype: section

    # - displayname: Max P value
    #   paramtype: text
    #   nf_paramname: max_pval
    #   formplaceholder: Enter the max_pval. Used for the compound class comparisons
    #   formvalue: "0.05"
    #   optional: true