workflowdisplay.yaml

name: classical_networking_workflow
displayname: STUFF
Views:
-   name: Files Summary
    displayname: Files Summary
    viewname: filesummary
    displaytype: datatable
    parameters:
        filename: nf_output/summaryresult.tsv
        columns:
            -   title: "Visualize"
                data: 
            -   title: "Filename"
                data: "Filename"
            -   title: "Vendor"
                data: "Vendor"
            -   title: "Model"
                data: "Model"
            -   title: "MS1s"
                data: "MS1s"
            -   title: "MS2s"
                data: "MS2s"
        columnDefs: '[ {"targets": 0,"data": null,"render": function ( data, type, row, meta ) {
        return `
            <a target="_blank" href="https://dashboard.gnps2.org/?usi=mzspec:GNPS2:TASK-${task}-input_spectra/${row["Filename"]}">View LCMS Run</a>
        `;}}]'

-   name: Cluster Summary
    displayname: Cluster Summary
    viewname: clustersummary
    displaytype: datatable_serverbig
    parameters:
        filename: nf_output/networking/clustersummary_with_network.tsv
        columns:
            -   title: "View"
                data: 
            -   title: "Cluster"
                data: "cluster index"
            -   title: "Parent mass"
                data: "parent mass"
            -   title: "# spectra"
                data: "number of spectra"
            -   title: "precursor charge"
                data: "precursor charge"
            -   title: "RTMean (Min)"
                data: "RTMean"
            -   title: "sum(precursor intensity)"
                data: "sum(precursor intensity)"
            -   title: "Compound Name"
                data: "Compound_Name"
            -   title: "Network Component"
                data: "component"
        columnDefs: '[ {"targets": 0,"data": null,"render": function ( data, type, row, meta ) {
        var filterdict = {
            type: "select",
            param: row["cluster index"],
            column: "#ClusterIdx"
        };
        return `
            <a target="_blank" href="https://metabolomics-usi.gnps2.org/dashinterface/?usi1=mzspec:GNPS2:TASK-${task}-nf_output/clustering/specs_ms.mgf:scan:${row["cluster index"]}">View Spectrum</a>
            <br>
            <a target="_blank" href="/result?viewname=rawspectra&filter=${encodeURIComponent(JSON.stringify([filterdict]))}&task=${task}">View Raw Spectra in Cluster</a>
            <br>
            <a target="_blank" href="/dashboards/networkviewer?usi=mzdata:GNPS2:TASK-${task}-nf_output/networking/components/component_${row["component"]}.graphml&usi-mgf=mzdata:GNPS2:TASK-${task}-nf_output/clustering/specs_ms.mgf">View Network Component</a>
        `;}},
        {"targets": 8,"data": "component","render": function ( data, type, row, meta ) {
        return `
            ${row["component"]}
            <br>
            <a target="_blank" href="https://multiplealignment.gnps2.org/setscreation/?task=${task}&component=${row["component"]}">View Component Alignment</a>
        `;}}]'

-   name: Library Match Results
    displayname: Library Match Results
    viewname: librarymatches
    displaytype: datatable #datatable
    parameters:
        filename: nf_output/library/merged_results_with_gnps.tsv
        columns:
            -   title: "View"
                data: 
            -   title: "#Scan#"
                data: "#Scan#"
            -   title: "Compound_Name"
                data: "Compound_Name"
            -   title: "Ion"
                data: Ion_Source
            -   title: "Precursor m/z"
                data: SpecMZ
            -   title: "Cosine"
                data: MQScore
            -   title: "Shared Peaks"
                data: SharedPeaks
            -   title: "MassDiff"
                data: MassDiff
            -   title: "Adduct"
                data: Adduct
            -   title: "SpectrumID"
                data: SpectrumID
            -   title: "Smiles"
                data: Smiles
            -   title: "Library Name"
                data: LibraryName
            -   title: "Library Scan"
                data: LibScan
        columnDefs: '[ {"targets": 0,"data": null,"render": function ( data, type, row, meta ) {
        if (row["SpectrumID"] && row["SpectrumID"].includes("CCMSLIB")) {
            return `
                <a target="_blank" href="https://metabolomics-usi.gnps2.org/dashinterface/?usi1=mzspec:GNPS2:TASK-${task}-nf_output/clustering/specs_ms.mgf:scan:${row["#Scan#"]}&usi2=mzspec:GNPS:GNPS-LIBRARY:accession:${row["SpectrumID"]}">View Mirror</a>
            `;
        }
        return `
            <a target="_blank" href="https://metabolomics-usi.gnps2.org/dashinterface/?usi1=mzspec:GNPS2:TASK-${task}-nf_output/clustering/specs_ms.mgf:scan:${row["#Scan#"]}&usi2=mzspec:GNPS2:TASK-${task}-input_libraries/${row["LibraryName"]}:scan:${row["LibScan"]}">View Mirror</a>
        `;}},
        {"targets": 2,"data": null,"render": function ( data, type, row, meta ) {
        var name = row["Compound_Name"] || "";
        var match = name.match(/LMFA\d{8}/);
        if (match) {
            return `<a target="_blank" href="https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/html/library_linkout.html?accession=${match[0]}">${name}</a>`;
        }
        return name;
        }},
        {"targets": 10,"data": null,"render": function ( data, type, row, meta ) {
        return `
            <img src="https://structure.gnps2.org/structureimg?smiles=${encodeURIComponent(row["Smiles"])}"/>
        `;}},
        {"targets": [11, 12], "visible": false}]'



-   name: Network Components List
    displayname: Network Components List
    viewname: networkcomponents
    displaytype: datatable_serverbig
    parameters:
        filename: nf_output/networking/component_summary.tsv
        columns:
            -   title: "View"
                data: 
            -   title: "Component Number"
                data: "component_id"
            -   title: "Number of Nodes"
                data: "number_of_nodes"
            -   title: "Number of Edges"
                data: "number_of_edges"
        columnDefs: '[ {"targets": 0,"data": null,"render": function ( data, type, row, meta ) {
        return `
            <a target="_blank" href="/dashboards/networkviewer?usi=mzdata:GNPS2:TASK-${task}-nf_output/networking/components/component_${row["component_id"]}.graphml&usi-mgf=mzdata:GNPS2:TASK-${task}-nf_output/clustering/specs_ms.mgf">View Network Component</a>
            <br>
            <a target="_blank" href="https://multiplealignment.gnps2.org/setscreation/?task=${task}&component=${row["component_id"]}">View Component Alignment</a>
        `;}},]'

-   name: Raw Spectra List
    displayname: Raw Spectra List
    viewname: rawspectra
    displaytype: datatable_serverbig
    parameters:
        filename: nf_output/clustering/clusterinfo.tsv
        columns:
            -   title: "View"
                data: 
            -   title: "Cluster"
                data: "#ClusterIdx"
            -   title: "Filename"
                data: "#Filename"
            -   title: "Scan"
                data: "#Scan"
            -   title: "Parent Mass"
                data: "#ParentMass"
            -   title: "Charge"
                data: "#Charge"
            -   title: "RT"
                data: "#RetTime"
            -   title: "PrecIntensity"
                data: "#PrecIntensity"
        columnDefs: '[ {"targets": 0,"data": null,"render": function ( data, type, row, meta ) {
        return `
            <a target="_blank" href="https://metabolomics-usi.gnps2.org/dashinterface/?usi1=mzspec:GNPS2:TASK-${task}-${row["#Filename"]}:scan:${row["#Scan"]}">View Original Spectrum</a>
            <br>
            <a target="_blank" href="https://metabolomics-usi.gnps2.org/dashinterface/?usi1=mzspec:GNPS2:TASK-${task}-${row["#Filename"]}:scan:${row["#Scan"]}&usi2=mzspec:GNPS2:TASK-${task}-nf_output/clustering/specs_ms.mgf:scan:${row["#ClusterIdx"]}">View Mirror</a>
            <br>
            <a target="_blank" href="https://dashboard.gnps2.org/?usi=mzspec:GNPS2:TASK-${task}-${row["#Filename"]}&xic_mz=${row["#ParentMass"]}&xic_rt=${row["#RetTime"]}">View LCMS Run</a>
        `;}}]'


-   name: Network Pairs List
    displayname: Network Pairs List
    viewname: pairslist
    displaytype: datatable_serverbig
    parameters:
        filename: nf_output/networking/pairs_with_components.tsv
        columns:
            -   title: "View"
                data: 
            -   title: "CLUSTERID1"
                data: CLUSTERID1
            -   title: "CLUSTERID2"
                data: CLUSTERID2
            -   title: "DeltaMZ"
                data: DeltaMZ
            -   title: "Cosine"
                data: Cosine
            -   title: "MatchedPeaks"
                data: MatchedPeaks
            -   title: "ComponentIndex"
                data: ComponentIndex
        columnDefs: '[ {"targets": 0,"data": null,"render": function ( data, type, row, meta ) {
        return `
            <a target="_blank" href="https://metabolomics-usi.gnps2.org/dashinterface/?usi1=mzspec:GNPS2:TASK-${task}-nf_output/clustering/specs_ms.mgf:scan:${row["CLUSTERID1"]}&usi2=mzspec:GNPS2:TASK-${task}-nf_output/clustering/specs_ms.mgf:scan:${row["CLUSTERID2"]}">View Mirror</a>
        `;}}]'

                
-   name: section
    displayname: Network Visualizations
    viewname: section
    displaytype: section

-   name: Visualize Network in Browser
    displayname: Visualize Full Network in Browser
    viewname: visualizefullnetwork
    displaytype: linkout
    parameters:
        baseurl: /dashboards/networkviewer
        urlparam:
            -   usi:mzdata:GNPS2:TASK-[task]-nf_output/networking/network.graphml
            -   usi-mgf:mzdata:GNPS2:TASK-[task]-nf_output/clustering/specs_ms.mgf

-   name: Visualize Network w/ Singletons in Browser
    displayname: Visualize Full Network w/ Singletons in Browser
    viewname: visualizefullsingletonnetwork
    displaytype: linkout
    parameters:
        baseurl: /dashboards/networkviewer
        urlparam:
            -   usi:mzdata:GNPS2:TASK-[task]-nf_output/networking/network_singletons.graphml
            -   usi-mgf:mzdata:GNPS2:TASK-[task]-nf_output/clustering/specs_ms.mgf

-   name: Export Network in Cytoscape
    displayname: Export Network in Cytoscape
    viewname: visualizecytoscape
    displaytype: linkout
    parameters:
        baseurl: https://cytoscape.gnps2.org/process
        urlparam:
            -   task:[task]

-   name: Export Network in Cytoscape with Singletons
    displayname: Export Network in Cytoscape with Singletons
    viewname: visualizecytoscapesingleton
    displaytype: linkout
    parameters:
        baseurl: https://cytoscape.gnps2.org/process
        urlparam:
            -   task:[task]
            -   override_path:nf_output/networking/network_singletons.graphml

-   name: section
    displayname: Downstream Analysis
    viewname: section
    displaytype: section

-   name: Downstream Analysis - Run Transitive Alignments
    displayname: Downstream Analysis - Run Transitive Alignments
    viewname: downstreamtransitive
    displaytype: linkout
    parameters:
        baseurl: /workflowinput
        urlparam:
            -   workflowname:Transitive_alignment_workflow
        hashparam:
            -   input_graphml:TASKLOCATION/[task]/nf_output/networking/network_singletons.graphml
            -   input_pairs:TASKLOCATION/[task]/nf_output/networking/merged_pairs.tsv
            -   input_spectra:TASKLOCATION/[task]/nf_output/clustering/specs_ms.mgf
            -   description:Downstream from [task] Classical Molecular Networking

-   name: Downstream Analysis - Overlay Custom Network
    displayname: Downstream Analysis - Overlay Custom Network
    viewname: downstreamoverlay
    displaytype: linkout
    parameters:
        baseurl: /workflowinput
        urlparam:
            -   workflowname:gnps2_network_overlay_workflow
        hashparam:
            -   input_graphml:TASKLOCATION/[task]/nf_output/networking/network_singletons.graphml
            -   input_mgf:TASKLOCATION/[task]/nf_output/clustering/specs_ms.mgf
            -   description:Downstream from [task] Classical Molecular Networking

# CMMC
-   name: Downstream Analysis - CMMC Enrichment Analysis
    displayname: Downstream Analysis - CMMC Enrichment Analysis
    viewname: downstreamcmmc
    displaytype: linkout
    parameters:
        baseurl: /workflowinput
        urlparam:
            -   workflowname:cmmc_gnps_network_enrichment_workflow
        hashparam:
            -   gnps2_graphml:TASKLOCATION/[task]/nf_output/networking/network_singletons.graphml
            -   gnps2_mgf:TASKLOCATION/[task]/nf_output/clustering/specs_ms.mgf
            -   networktype:CLASSICAL
            -   datasource:GNPS2
            -   description:Downstream from [task] Classical Molecular Networking

-   name: Downstream Analysis - Feature Augment Network
    displayname: Downstream Analysis - Feature Augment Network
    viewname: downstreamfeatureaugment
    displaytype: linkout
    parameters:
        baseurl: /workflowinput
        urlparam:
            -   workflowname:feature_augmentation_workflow
        hashparam:
            -   input_features:TASKLOCATION/[task]/nf_output/clustering/featuretable_reformatted_presence.csv
            -   input_spectra:TASKLOCATION/[task]/input_spectra
            -   description:Downstream from [task] Classical Molecular Networking

-   name: PostNetworking - MassQL Interactive Analysis
    displayname: PostNetworking - MassQL Interactive Analysis
    viewname: massqlpostmn
    displaytype: linkout
    parameters:
        baseurl: "https://massqlpostmn.gnps2.org"
        urlparam:
            -   task_id:[task]


-   name: ModiFinder - Localize Analog Modifications
    displayname: ModiFinder - Localize Analog Modifications
    viewname: high_throughput_modifinder
    displaytype: linkout
    parameters:
        baseurl: /workflowinput
        urlparam:
            -   workflowname:high_throughput_modifinder
        hashparam:
            -   matches_path:TASKLOCATION/[task]/nf_output/modifinder_input.csv
            -   with_library_search:"0"

-   name: PostNetworking - MassQL Interactive Analysis
    displayname: PostNetworking - MassQL Interactive Analysis
    viewname: massqlpostmn
    displaytype: linkout
    parameters:
        baseurl: "https://massqlpostmn.gnps2.org"
        urlparam:
            -   task_id:[task]

-   name: section
    displayname: Download Network Files
    viewname: section
    displaytype: section

-   name: Download Network GraphML
    displayname: Download Network GraphML
    viewname: graphml
    displaytype: download
    parameters:
        filename: nf_output/networking/network.graphml

-   name: Download Network with Singletons GraphML
    displayname: Download Network with Singletons GraphML
    viewname: graphmlsingletons
    displaytype: download
    parameters:
        filename: nf_output/networking/network_singletons.graphml

-   name: Download Consensus MS/MS MGF
    displayname: Download Consensus MS/MS MGF
    viewname: specms
    displaytype: download
    parameters:
        filename: nf_output/clustering/specs_ms.mgf

-   name: Download Merged Metadata File
    displayname: Download Merged Metadata File
    viewname: metadatadownload
    displaytype: download
    parameters:
        filename: nf_output/metadata/merged_metadata.tsvtsv