LibrarySearch_Workflow/workflowdisplay.yaml at master · Wang-Bioinformatics-Lab/LibrarySearch_Workflow · GitHub

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name: librarysearch_workflow
displayname: STUFF
Views:
-   name: Search Results List
    displayname: Search Results List
    viewname: summarylist
    displaytype: datatable_serverbig #datatable
    parameters:
        filename: nf_output/merged_results_with_gnps.tsv
        columns:
            -   title: "View Spectra"
                data:
            -   title: "Use ModiFinder"
                data:
            -   title: "Query Scan"
                data: "#Scan#"
            -   title: "Query File"
                data: SpectrumFile
            -   title: "Name"
                data: Compound_Name
            -   title: "Ion"
                data: Ion_Source
            -   title: "Precursor m/z"
                data: SpecMZ
            -   title: "Similarity Score"
                data: MQScore
            -   title: "Shared Peaks"
                data: SharedPeaks
            -   title: "MassDiff"
                data: MassDiff
            -   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-${task}-inputspectra/${row["SpectrumFile"]}: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-${task}-inputspectra/${row["SpectrumFile"]}:scan:${row["#Scan#"]}&usi2=mzspec:GNPS2:TASK-${task}-input_libraries/${row["LibraryName"]}:scan:${row["LibScan"]}">View Mirror</a>
        `;}},
        {
            "targets": 1, "data": null, "render": function ( data, type, row, meta ) {
                return row["Smiles"]? `<a target="_blank" href="https://modifinder.gnps2.org/?USI1=mzspec:GNPS:GNPS-LIBRARY:accession:${row["SpectrumID"]}&USI2=mzspec:GNPS2:TASK-${task}-inputspectra/${row["SpectrumFile"]}:scan:${row["#Scan#"]}&SMILES1=${row["Smiles"]}">Check on ModiFinder</a>` : `<p>Unknown Structure</p>`;
            }},
        {"targets": 11,"data": null,"render": function ( data, type, row, meta ) {
        return `
            <img src="https://structure.gnps2.org/structureimg?smiles=${row["Smiles"]}"/>
        `;}},
        {"targets": [10, 11], "visible": false}]'


-   name: Search Results Top 1 List
    displayname: Search Results Top 1 List
    viewname: summarylist1
    displaytype: datatable_serverbig #datatable
    parameters:
        filename: nf_output/merged_results_with_gnps_top1.tsv
        columns:
            -   title: "View Spectra"
                data:
            -   title: "Use ModiFinder"
                data:
            -   title: "Query Scan"
                data: "#Scan#"
            -   title: "Query File"
                data: SpectrumFile
            -   title: "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: "SpectrumID"
                data: SpectrumID
            -   title: "Smiles"
                data: Smiles
        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-${task}-inputspectra/${row["SpectrumFile"]}:scan:${row["#Scan#"]}&usi2=mzspec:GNPS:GNPS-LIBRARY:accession:${row["SpectrumID"]}">View Mirror</a>
        `;}},
        {
            "targets": 1, "data": null, "render": function ( data, type, row, meta ) {
                return row["Smiles"]? `<a target="_blank" href="https://modifinder.gnps2.org/?USI1=mzspec:GNPS:GNPS-LIBRARY:accession:${row["SpectrumID"]}&USI2=mzspec:GNPS2:TASK-${task}-inputspectra/${row["SpectrumFile"]}:scan:${row["#Scan#"]}&SMILES1=${row["Smiles"]}">Check on ModiFinder</a>` : `<p>Unknown Structure</p>`;
            }},
        {"targets": 11,"data": null,"render": function ( data, type, row, meta ) {
        return `
            <img src="https://structure.gnps2.org/structureimg?smiles=${row["Smiles"]}"/>
        `;}},
        ]'