workflowinput.yaml

workflowname: libraryanalogsearch_accelerated_workflow
workflowdescription: libraryanalogsearch_accelerated_workflow
workflowlongdescription: Library analog search accelerated with BLINK
workflowversion: "0.1"
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: Input Data Folder
      paramtype: fileselector
      nf_paramname: inputspectra
      formplaceholder: Enter the path to search data
      formvalue: ""
      targettaskfolder: inputspectra
      optional: false
      selectsinglefile: false
      folderunroll: true

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

    - displayname: Search Parameters
      paramtype: section

    - displayname: Ion Mode
      paramtype: select
      nf_paramname: blink_ionization
      formvalue: positive
      options:
        - value: positive
          display: positive
        - value: negative
          display: negative

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

    - 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"

    - displayname: Analog Max Shift
      paramtype: text
      nf_paramname: analog_max_shift
      formplaceholder: Enter the analog_max_shift
      formvalue: "200"

    - displayname: Top-K
      paramtype: text
      nf_paramname: topk
      formplaceholder: Enter the topk
      formvalue: "1"