{  "preview": [
        {
            "title":"Preview",
            "link":"preview-tree", 
            "file": "preview.newick", 
            "type": "tree",
            "comment": "",
            "style": ""
        },
        {   "file":"seqdata.txt", 
            "title":"Sequence Data", 
            "link": "sequence-data", 
            "type" : "table",
            "comment": "",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title": "Reads", "field":"Reads","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Yield", "field":"Yield","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"GC content", "field":"GC content","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Min len", "field":"Min len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Avg len", "field":"Avg len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Max len", "field":"Max len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Average quality (% >Q30)", "field":"Average quality (% >Q30)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Estimated average depth", "field":"Estimated average depth","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file":"species.txt", 
            "title": "Species Identification", 
            "type": "table", 
            "link":"species-identification",
            "comment": "",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title":"Match 1", "field":"Match 1","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_1 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Match 2", "field":"Match 2","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_2 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Match 3", "field":"Match 3","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_3 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        }
        ],
    "default":[
        {   "title": "Phylogeny", 
            "link":"phylogeny", 
            "file": "core.newick", 
            "type": "tree",
            "style": ""
        },
        {   "file":"seqdata.txt", 
            "title":"Sequence Data", 
            "link": "sequence-data", 
            "type" : "table",
            "comment": "",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title": "Reads", "field":"Reads","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Yield", "field":"Yield","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"GC content", "field":"GC content","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Min len", "field":"Min len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Avg len", "field":"Avg len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Max len", "field":"Max len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Average quality (% >Q30)", "field":"Average quality (% >Q30)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Estimated average depth", "field":"Estimated average depth","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file":"species.txt", 
            "title": "Species Identification", 
            "type": "table", 
            "link":"species-identification",
            "comment": "",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title":"Match 1", "field":"Match 1","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_1 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Match 2", "field":"Match 2","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_2 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Match 3", "field":"Match 3","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_3 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file": "core_genome.txt", 
            "title": "Core Genome", 
            "link":"core-genome", 
            "type":"table",
            "comment": "",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title":"Length", "field":"Length","headerFilter":"input"},
                {"title": "Aligned", "field":"Aligned","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Unaligned", "field":"Unaligned","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "Heterozygous", "field":"Heterozygous","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Low coverage", "field":"Low coverage","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "% Aligned", "field":"% Aligned","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file": "distances.tab", 
            "title":"SNP distances", 
            "type":"matrix", 
            "link":"snp-distances",
            "comment": "",
            "columns":[]
        },
        {   "file":"mlst.txt", 
            "title":"MLST", 
            "type":"table", 
            "link":"mlst",
            "comment": "",
            "columns":[]
        },
        {   "file":"resistome.txt", 
            "title":"Resistome", 
            "type":"table", 
            "link":"resistome",
            "comment": "Note: * indicates a <90% match (identity and coverage) <100%, ^ indicates > 50% < 90% coverage >90% identity. ",
            "columns":[]
        },
        {   "file":"virulome.txt", 
            "title":"Virulome", 
            "type":"table", 
            "link":"virulome",
            "comment": "Note: * indicates a <90% match (identity and coverage) <100%, ^ indicates > 50% < 90% coverage >90% identity. ",
            "columns":[]
        },
        {   "file": "assembly.txt", 
            "title":"Assembly", 
            "type":"table", 
            "link":"assembly",
            "comment":"",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title":"bp", "field":"bp","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "# Contigs", "field":"# Contigs","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"# Gaps", "field":"# Gaps","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "Min Contigs size", "field":"Min Contig size","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "Avg Contigs size", "field":"Max Contig size","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "N50", "field":"N50","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "CDS", "field":"CDS","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "rRNA", "field":"rRNA","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file": "plasmid.txt", 
            "title":"Plasmid", 
            "type":"table", 
            "link":"plasmid",
            "comment":"",
            "columns":[]
        }
    ],
    "pluspan":[
        {   "title": "Phylogeny", 
            "link":"phylogeny", 
            "file": "core.newick", 
            "type": "tree",
            "style": ""
        },
        {   "file":"summary_statistics.txt", 
            "title":"Pan Genome", 
            "type": "table", 
            "image": "pan_genome.svg", 
            "link":"pan-genome",
            "comment":"",
            "columns":[
                {"title":"Genes","field":"Genes"},
                {"title": "Range", "field":"Range"},
                {"title": "Total", "field": "Total"}]
        },
        {   "file":"seqdata.txt", 
            "title":"Sequence Data", 
            "link": "sequence-data", 
            "type" : "table",
            "comment": "",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title": "Reads", "field":"Reads","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Yield", "field":"Yield","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"GC content", "field":"GC content","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Min len", "field":"Min len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Avg len", "field":"Avg len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Max len", "field":"Max len","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Average quality (% >Q30)", "field":"Average quality (% >Q30)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Estimated average depth", "field":"Estimated average depth","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file":"species.txt", 
            "title": "Species Identification", 
            "type": "table", 
            "link":"species-identification",
            "comment": "",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title":"Match 1", "field":"Match 1","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_1 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Match 2", "field":"Match 2","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_2 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Match 3", "field":"Match 3","headerFilter":"input","headerFilterPlaceholder":"Search species"},
                {"title": "Detected (%)", "field":"Detected_3 (%)","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file": "core_genome.txt", 
            "title": "Core Genome", 
            "link":"core-genome", 
            "type":"table",
            "comment": "",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title":"Length", "field":"Length","headerFilter":"input"},
                {"title": "Aligned", "field":"Aligned","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Unaligned", "field":"Unaligned","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "Heterozygous", "field":"Heterozygous","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"Low coverage", "field":"Low coverage","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "% Aligned", "field":"% Aligned","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file": "distances.tab", 
            "title":"SNP distances", 
            "type":"matrix", 
            "link":"snp-distances",
            "comment": "",
            "columns":[]
        },
        {   "file":"mlst.txt", 
            "title":"MLST", 
            "type":"table", 
            "link":"mlst",
            "comment": "",
            "columns":[]
        },
        {   "file":"resistome.txt", 
            "title":"Resistome", 
            "type":"table", 
            "link":"resistome",
            "comment": "Note: * indicates a <90% match (identity and coverage) <100%, ^ indicates > 50% < 90% coverage >90% identity. ",
            "columns":[]
        },
        {   "file":"virulome.txt", 
            "title":"Virulome", 
            "type":"table", 
            "link":"virulome",
            "comment": "Note: * indicates a <90% match (identity and coverage) <100%, ^ indicates > 50% < 90% coverage >90% identity. ",
            "columns":[]
        },
        {   "file": "assembly.txt", 
            "title":"Assembly", 
            "type":"table", 
            "link":"assembly",
            "comment":"",
            "columns" : [
                {"title":"Isolate","field":"Isolate","headerFilter":"input","headerFilterPlaceholder":"Search isolate"},
                {"title":"bp", "field":"bp","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "# Contigs", "field":"# Contigs","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title":"# Gaps", "field":"# Gaps","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "Min Contigs size", "field":"Min Contig size","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "Avg Contigs size", "field":"Max Contig size","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "N50", "field":"N50","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "CDS", "field":"CDS","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="},
                {"title": "rRNA", "field":"rRNA","headerFilter":"number", "headerFilterPlaceholder":"at least...", "headerFilterFunc":">="}
                ]
        },
        {   "file": "plasmid.txt", 
            "title":"Plasmid", 
            "type":"table", 
            "link":"plasmid",
            "comment":"",
            "columns":[]
        }
    ]
        
}
    