workflowinput.yaml

workflowname: librarysearch_workflow
workflowdescription: librarysearch_workflow
workflowlongdescription: This is a library search workflow for GNPS2
workflowversion: "2025.02.21"
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
      options:
        - value: gnps
          display: gnps
        - value: gnps_new
          display: gnps_new
        - value: blink
          display: blink

    - displayname: Precursor Ion Tolerance
      paramtype: text
      nf_paramname: pm_tolerance
      formplaceholder: Enter the pm_tolerance
      formvalue: "2.0"
      tooltip: "pm_tolerance"
      showif:
        - condition:
          - key: searchtool
            value: gnps
        - condition:
          - key: searchtool
            value: gnps_new

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

    - 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

    # 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

    - 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