workflowinput.yaml

workflowname: feature_based_molecular_networking_workflow
workflowdescription: feature_based_molecular_networking_workflow
workflowlongdescription: This is a feature_based_molecular_networking_workflow workflow for GNPS2
workflowversion: "2026.03.19"
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: Input inputfeatures
      paramtype: fileselector
      nf_paramname: inputfeatures
      formplaceholder: Enter the path to inputfeatures
      formvalue: ""
      targettaskfolder: inputfeatures
      optional: false
      selectsinglefile: true
      folderunroll: true

    - displayname: Input inputspectra
      paramtype: fileselector
      nf_paramname: inputspectra
      formplaceholder: Enter the path to inputspectra
      formvalue: ""
      targettaskfolder: inputspectra
      optional: false
      selectsinglefile: false
      folderunroll: true
    
    - displayname: Input Metadata File
      paramtype: fileselector
      nf_paramname: metadata_filename
      formplaceholder: Enter the path to metadata_filename
      formvalue: ""
      targettaskfolder: metadata_filename
      optional: true
      selectsinglefile: true
      folderunroll: true
    
    - displayname: Input Spectral Library Folder
      paramtype: fileselector
      nf_paramname: input_libraries
      formplaceholder: Enter the path to input_libraries
      formvalue: "LIBRARYLOCATION/LC/LIBRARY"
      targettaskfolder: input_libraries
      optional: false
      selectsinglefile: false
      folderunroll: true

    - displayname: Feature Finding Tool
      paramtype: select
      nf_paramname: featurefindingtool
      formvalue: MZMINE
      options:
        - value: MZMINE
          display: MZMINE
        - value: OPENMS
          display: OPENMS
        - value: PROGENESIS
          display: PROGENESIS
        - value: XCMS3
          display: XCMS3
        - value: METABOSCAPE
          display: METABOSCAPE
        - value: MSDIAL
          display: MSDIAL
        - value: MSDIAL5
          display: MSDIAL5
        - value: OPTIMUS
          display: OPTIMUS
        - value: AGILENT
          display: AGILENT (Legacy)
        - value: AGILENT2
          display: AGILENT2
        - value: AGILENT_EXPLORER2
          display: AGILENT_EXPLORER2
        - value: MZTABM
          display: MAZTABM

    - displayname: Additional Edges
      paramtype: section

    - displayname: Input Additional Supplemental Edges File(s) (Optional)
      paramtype: fileselector
      nf_paramname: input_supplemental_edges
      formplaceholder: Enter the path to supplemental edges
      formvalue: ""
      targettaskfolder: input_supplemental_edges
      optional: true
      selectsinglefile: false
      folderunroll: true

    - displayname: Raw Data Selection
      paramtype: section

    - displayname: Input Raw Data Folder (Optional)
      paramtype: fileselector
      nf_paramname: input_raw_spectra
      formplaceholder: Enter the path to data
      formvalue: ""
      targettaskfolder: input_raw_spectra
      optional: true
      selectsinglefile: false
      folderunroll: true

    - displayname: General Parameters
      paramtype: section

    - displayname: Precursor Ion Tolerance
      paramtype: text
      nf_paramname: pm_tolerance
      formplaceholder: Enter the pm_tolerance
      formvalue: "2.0"
      tooltip: "pm_tolerance"

    - displayname: Fragment Ion Tolerance
      paramtype: text
      nf_paramname: fragment_tolerance
      formplaceholder: Enter the fragment_tolerance
      formvalue: "0.5"
      tooltip: "fragment_tolerance"

    - displayname: Advanced Filtering Parameters
      paramtype: section

    # - displayname: Min Peak Intensity
    #   paramtype: text
    #   nf_paramname: min_peak_intensity
    #   formplaceholder: Enter the min_peak_intensity
    #   formvalue: "0.0"
    #   tooltip: "min_peak_intensity"
    
    - displayname: Window Filter
      paramtype: select
      nf_paramname: window_filter
      formvalue: "1"
      options:
        - value: "1"
          display: "yes"
        - value: "0"
          display: "no"

    - displayname: Precursor Window Filter
      paramtype: select
      nf_paramname: precursor_filter
      formvalue: "1"
      options:
        - value: "1"
          display: "yes"
        - value: "0"
          display: "no"

    - displayname: Networking Parameters
      paramtype: section

    - displayname: min_cosine
      paramtype: text
      nf_paramname: networking_min_cosine
      formplaceholder: Enter the min_cosine
      formvalue: "0.7"

    - displayname: min_matched_peaks
      paramtype: text
      nf_paramname: networking_min_matched_peaks
      formplaceholder: Enter the min_matched_peaks
      formvalue: "6"

    - displayname: networking_max_shift
      paramtype: text
      nf_paramname: networking_max_shift
      formplaceholder: Enter the networking_max_shift
      formvalue: "1999"

    
    - displayname: Network Topology Parameters
      paramtype: section

    - displayname: Classic Param - Top K
      paramtype: text
      nf_paramname: topology_topk
      formplaceholder: Enter the topology_topk
      formvalue: "10"

    - displayname: Classic Param - Max Component Size
      paramtype: text
      nf_paramname: topology_maxcomponent
      formplaceholder: Enter the topology_maxcomponent
      formvalue: "100"

    - displayname: Library Search Parameters
      paramtype: section

    - displayname: Library Minimum Cosine
      paramtype: text
      nf_paramname: library_min_cosine
      formplaceholder: Enter the library_min_cosine
      formvalue: "0.7"

    - displayname: Library Minimum Matched Peaks
      paramtype: text
      nf_paramname: library_min_matched_peaks
      formplaceholder: Enter the library_min_matched_peaks
      formvalue: "6"

    # Analog Search
    - displayname: Analog Search
      paramtype: select
      nf_paramname: library_analog_search
      formvalue: "0"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"

    - displayname: Analog Search Max Shift
      paramtype: text
      nf_paramname: library_analog_max_shift
      formplaceholder: Enter the max mass shift
      formvalue: "1999"

    - displayname: Top-K
      paramtype: text
      nf_paramname: library_topk
      formplaceholder: Enter the topk
      formvalue: "1"
    
    
    - displayname: Normalization Parameters
      paramtype: section

    - displayname: Quantification Normalization
      paramtype: select
      nf_paramname: normalization
      formvalue: "None"
      options:
        - value: "None"
          display: "None"
        - value: "RowSum"
          display: "RowSum"