workflowinput.yaml

workflowname: librarysearch_workflow
workflowdescription: librarysearch_workflow
workflowlongdescription: This is a library search workflow for GNPS2. GNPS Indexed is the default now that should have the same performance as before but significantly faster. Additionally - the filtering of queries and library is on by default for precursor filtering and window filtering. 
workflowversion: "2026.03.24"
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 Data Folder
      paramtype: fileselector
      nf_paramname: inputspectra
      formplaceholder: Enter the path to search data
      formvalue: ""
      targettaskfolder: inputspectra
      optional: false
      selectsinglefile: false
      folderunroll: false

    - displayname: Input Library Folder
      paramtype: fileselector
      nf_paramname: inputlibraries
      formplaceholder: Enter the path to search libraries
      formvalue: "LIBRARYLOCATION/LC/LIBRARY"
      targettaskfolder: inputlibraries
      optional: false
      selectsinglefile: false
      folderunroll: true

    - displayname: Search Parameters
      paramtype: section

    - displayname: Search Tool
      paramtype: select
      nf_paramname: searchtool
      formvalue: gnps_indexed
      options:
        - value: gnps
          display: gnps
        - value: gnps_new
          display: gnps_new
        - value: blink
          display: blink
        - value: gnps_indexed
          display: gnps_indexed

    - displayname: Precursor Ion Tolerance
      paramtype: text
      nf_paramname: pm_tolerance
      formplaceholder: Enter the pm_tolerance
      formvalue: "0.05"
      tooltip: "pm_tolerance"
      showif:
        - condition:
          - key: searchtool
            value: gnps
        - condition:
          - key: searchtool
            value: gnps_new
        - condition:
          - key: searchtool
            value: gnps_indexed

    - displayname: Filter Precursor
      paramtype: select
      nf_paramname: filter_precursor
      formvalue: "1"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"
      tooltip: "filter precursor peaks and peaks around precursor m/z"
      showif:
        - condition:
          - key: searchtool
            value: gnps
        - condition:
          - key: searchtool
            value: gnps_indexed

    - displayname: Window Filter
      paramtype: select
      nf_paramname: filter_window
      formvalue: "1"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"
      tooltip: "If `Yes`, for each peak, it will check a window around that peak, if it is not one of the top peaks in terms of intensity in that window, it will be filtered out. This will speed up the search and reduce the effect of noise."
      showif:
        - condition:
          - key: searchtool
            value: gnps
        - condition:
          - key: searchtool
            value: gnps_indexed

    - displayname: Fragment Ion Tolerance
      paramtype: text
      nf_paramname: fragment_tolerance
      formplaceholder: Enter the fragment_tolerance
      formvalue: "0.05"
      tooltip: "fragment_tolerance"
      

    - displayname: Library Minimum Similarity Score
      paramtype: text
      nf_paramname: library_min_similarity
      formplaceholder: Enter the library minimum similarity score
      formvalue: "0.7"
      showif:
        - condition:
          - key: searchtool
            value: gnps
        - condition:
          - key: searchtool
            value: gnps_new
        - condition:
          - key: searchtool
            value: gnps_indexed

    - displayname: Library Minimum Matched Peaks
      paramtype: text
      nf_paramname: library_min_matched_peaks
      formplaceholder: Enter the library_min_matched_peaks
      formvalue: "6"
      showif:
        - condition:
          - key: searchtool
            value: gnps
        - condition:
          - key: searchtool
            value: gnps_new
        - condition:
          - key: searchtool
            value: gnps_indexed

    # Analog Search
    - displayname: Analog Search
      paramtype: select
      nf_paramname: analog_search
      formvalue: "0"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"
      showif:
        - condition:
          - key: searchtool
            value: gnps
        - condition:
          - key: searchtool
            value: gnps_new
        - condition:
          - key: searchtool
            value: gnps_indexed
    
    - displayname: Top-K
      paramtype: text
      nf_paramname: topk
      formplaceholder: Enter the topk
      formvalue: "1"

    - displayname: Filter Only To Compounds with Structures
      paramtype: select
      nf_paramname: filtertostructures
      formplaceholder: Enter the topk
      formvalue: "0"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"


    - displayname: gnps_new Parameters
      paramtype: section
      showif:
        - condition:
          - key: searchtool
            value: gnps_new

    - displayname: Searching Algorithm
      paramtype: select
      nf_paramname: search_algorithm
      formvalue: cosine
      options:
        - value: cos
          display: cosine
        - value: rev_cos
          display: reverse cosine
        - value: entropy
          display: entropy similarity
        - value: rev_entropy
          display: reverse entropy similarity
      showif:
        - condition:
          - key: searchtool
            value: gnps_new

    - displayname: Peak intensity transformation
      paramtype: select
      nf_paramname: peak_transformation
      formvalue: sqrt
      options:
        - value: none
          display: No peak transformation applied
        - value: sqrt
          display: Square root transformation
      tooltip: "Sqrt transformation is only applied when (reverse) cosine similarity is used. Entropy similarity is not designed for transformed intensities."
      showif:
        - condition:
          - key: searchtool
            value: gnps_new

    - displayname: Unmatched peak penalty factor (for reverse search)
      paramtype: text
      nf_paramname: unmatched_penalty_factor
      formplaceholder: Enter the unmatched_penalty_factor (0-1, designed for reverse spectral search, peak intensity will be penalized by this factor if it is not matched)
      formvalue: "0.6"
      tooltip: "This only works for reverse search. Peak intensity will be penalized by this factor if it is unmatched. A factor of 0 means no penalty, ie. traditional cosine similarity. A factor of 1 means full penalty, ie. traditional reverse cosine similarity."
      showif:
        - condition:
          - key: searchtool
            value: gnps_new


    - displayname: Blink Parameters
      paramtype: section
      showif:
        - condition:
          - key: searchtool
            value: blink

    - displayname: Ion Mode
      paramtype: select
      nf_paramname: blink_ionization
      formvalue: positive
      options:
        - value: positive
          display: positive
        - value: negative
          display: negative
      showif:
        - condition:
          - key: searchtool
            value: blink

    - displayname: Minimum BLINK Predicted Score
      paramtype: text
      nf_paramname: blink_minpredict
      formplaceholder: Enter the blink_minpredict
      formvalue: "0.0075"
      tooltip: "blink_minpredict"
      showif:
        - condition:
          - key: searchtool
            value: blink

    - displayname: Force Offline Annotations (speeds up workflow)
      paramtype: select
      nf_paramname: forceoffline
      formvalue: "No"
      options:
        - value: "Yes"
          display: "Yes"
        - value: "No"
          display: "No"

    - displayname: Filtering Parameters
      paramtype: section
      showif:
        - condition:
          - key: searchtool
            value: gnps_indexed

    - displayname: Precursor Filtering
      paramtype: select
      nf_paramname: filter_precursor
      formvalue: "1"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"
      showif:
        - condition:
          - key: searchtool
            value: gnps_indexed

    - displayname: Window Filtering
      paramtype: select
      nf_paramname: filter_window
      formvalue: "1"
      options:
        - value: "0"
          display: "No"
        - value: "1"
          display: "Yes"
      showif:
        - condition:
          - key: searchtool
            value: gnps_indexed