annotate x/config.json @ 129:d08080933718 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6d8a6a308c219c112dbfc09fe48ad462746d6fb0

{
  "plugins": [
    {
      "name": "BedScorePlugin",
      "umdLoc": {
        "uri": "bedscoreplugin.js"
      }
    },
    {
      "name": "MafViewer",
      "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
    }
  ],
  "configuration": {
    "disableAnalytics": false,
    "theme": {
      "palette": {
        "primary": {
          "main": "#0d233f"
        },
        "secondary": {
          "main": "#721e63"
        },
        "tertiary": {
          "main": "#135560"
        },
        "quaternary": {
          "main": "#ffb11d"
        }
      },
      "typography": {
        "fontSize": 10
      }
    }
  },
  "defaultSession": {
    "name": "New test session",
    "views": [
      {
        "type": "LinearGenomeView",
        "offsetPx": 0,
        "bpPerPx": 50,
        "minimized": false,
        "tracks": [
          {
            "type": "FeatureTrack",
            "configuration": "merlin.gff3_0",
            "displays": [
              {
                "type": "LinearBasicDisplay",
                "displayId": "merlin.gff3_0-LinearBasicDisplay",
                "trackShowLabels": false,
                "trackShowDescriptions": false,
                "configuration": "merlin.gff3_0-LinearBasicDisplay"
              }
            ]
          },
          {
            "type": "QuantitativeTrack",
            "configuration": "merlin.bw_1",
            "displays": [
              {
                "type": "LinearWiggleDisplay",
                "displayId": "merlin.bw_1-LinearWiggleDisplay",
                "color": "#135560",
                "autoscale": "globalsd",
                "resolution": 1,
                "summaryScoreMode": "whiskers",
                "filled": false,
                "scaleType": "linear",
                "displayCrossHatches": false,
                "configuration": "merlin.bw_1-LinearWiggleDisplay"
              }
            ]
          },
          {
            "type": "FeatureTrack",
            "configuration": "test-6.bed_2",
            "displays": [
              {
                "type": "LinearBasicDisplay",
                "displayId": "test-6.bed_2-LinearBasicDisplay",
                "trackShowLabels": false,
                "trackShowDescriptions": false,
                "configuration": "test-6.bed_2-LinearBasicDisplay"
              }
            ]
          },
          {
            "type": "VariantTrack",
            "configuration": "merlin.vcf_3",
            "displays": [
              {
                "type": "LinearVariantDisplay",
                "displayId": "merlin.vcf_3-LinearVariantDisplay",
                "trackShowLabels": false,
                "trackShowDescriptions": false,
                "configuration": "merlin.vcf_3-LinearVariantDisplay"
              }
            ]
          },
          {
            "type": "AlignmentsTrack",
            "configuration": "merlin.cram_4",
            "displays": [
              {
                "type": "LinearAlignmentsDisplay",
                "displayId": "merlin.cram_4-LinearAlignmentsDisplay",
                "configuration": "merlin.cram_4-LinearAlignmentsDisplay"
              }
            ]
          },
          {
            "type": "AlignmentsTrack",
            "configuration": "merlin-sample.bam_5",
            "displays": [
              {
                "type": "LinearAlignmentsDisplay",
                "displayId": "merlin-sample.bam_5-LinearAlignmentsDisplay",
                "configuration": "merlin-sample.bam_5-LinearAlignmentsDisplay"
              }
            ]
          },
          {
            "type": "MafTrack",
            "configuration": "merlinlastz.maf_6",
            "displays": [
              {
                "type": "LinearBasicDisplay",
                "displayId": "merlinlastz.maf_6-LinearBasicDisplay",
                "trackShowLabels": false,
                "trackShowDescriptions": false,
                "configuration": "merlinlastz.maf_6-LinearBasicDisplay"
              }
            ]
          },
          {
            "type": "FeatureTrack",
            "configuration": "merlin.blastxml_7",
            "displays": [
              {
                "type": "LinearBasicDisplay",
                "displayId": "merlin.blastxml_7-LinearBasicDisplay",
                "trackShowLabels": false,
                "trackShowDescriptions": false,
                "configuration": "merlin.blastxml_7-LinearBasicDisplay"
              }
            ]
          }
        ],
        "displayedRegions": [
          {
            "reversed": false,
            "assemblyName": "Merlin",
            "refName": "Merlin",
            "start": 0,
            "end": 172788
          }
        ]
      },
      {
        "type": "LinearGenomeView",
        "offsetPx": 0,
        "bpPerPx": 50,
        "minimized": false,
        "tracks": [
          {
            "type": "HicTrack",
            "configuration": "dm3test.cool_9",
            "displays": [
              {
                "type": "LinearHicDisplay",
                "configuration": "dm3test.cool_9-LinearHicDisplay"
              }
            ]
          }
        ],
        "displayedRegions": [
          {
            "reversed": false,
            "assemblyName": "dm3.fa",
            "refName": "NT_037436.4",
            "start": 0,
            "end": 28110227
          }
        ]
      },
      {
        "type": "LinearGenomeView",
        "offsetPx": 0,
        "bpPerPx": 50,
        "minimized": false,
        "tracks": [
          {
            "type": "SyntenyTrack",
            "configuration": "peach-grape-map.paf_10",
            "displays": [
              {
                "type": "LGVSyntenyDisplay",
                "displayId": "peach-grape-map.paf_10-LinearBasicDisplay",
                "configuration": "peach-grape-map.paf_10-LGVSyntenyDisplay"
              }
            ]
          },
          {
            "type": "SyntenyTrack",
            "configuration": "arabgrapepeach.paf_11",
            "displays": [
              {
                "type": "LGVSyntenyDisplay",
                "displayId": "arabgrapepeach.paf_11-LinearBasicDisplay",
                "configuration": "arabgrapepeach.paf_11-LGVSyntenyDisplay"
              }
            ]
          },
          {
            "type": "SyntenyTrack",
            "configuration": "arabgrapepeach.paf_12",
            "displays": [
              {
                "type": "LGVSyntenyDisplay",
                "displayId": "arabgrapepeach.paf_12-LinearBasicDisplay",
                "configuration": "arabgrapepeach.paf_12-LGVSyntenyDisplay"
              }
            ]
          }
        ],
        "displayedRegions": [
          {
            "reversed": false,
            "assemblyName": "Ppersica1.fa",
            "refName": "Pp01",
            "start": 0,
            "end": 47851208
          }
        ]
      },
      {
        "type": "LinearGenomeView",
        "offsetPx": 0,
        "bpPerPx": 50,
        "minimized": false,
        "tracks": [
          {
            "type": "HicTrack",
            "configuration": "humanhic_13",
            "displays": [
              {
                "type": "LinearHicDisplay",
                "configuration": "humanhic_13-LinearHicDisplay"
              }
            ]
          }
        ],
        "displayedRegions": [
          {
            "reversed": false,
            "assemblyName": "hg38",
            "refName": "1",
            "start": 0,
            "end": 248956422
          }
        ]
      }
    ]
  },
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "merlin.gff3_0",
      "name": "merlin.gff3_0",
      "assemblyNames": [
        "Merlin"
      ],
      "category": [
        "Assembly properties"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "merlin.gff3_0.gz"
        },
        "index": {
          "location": {
            "uri": "merlin.gff3_0.gz.tbi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "merlin.gff3_0-LinearBasicDisplay"
        },
        {
          "type": "LinearArcDisplay",
          "displayId": "merlin.gff3_0-LinearArcDisplay"
        }
      ],
      "style": {
        "type": "LinearBasicDisplay",
        "displayId": "merlin.gff3_0-LinearBasicDisplay",
        "trackShowLabels": false,
        "trackShowDescriptions": false,
        "configuration": "merlin.gff3_0-LinearBasicDisplay"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "merlin.bw_1",
      "name": "merlin.bw_1",
      "category": [
        "Assembly properties"
      ],
      "assemblyNames": [
        "Merlin"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "merlin.bw_1"
        }
      },
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "merlin.bw_1-LinearWiggleDisplay"
        }
      ],
      "style": {
        "type": "LinearWiggleDisplay",
        "displayId": "merlin.bw_1-LinearWiggleDisplay",
        "color": "#135560",
        "autoscale": "globalsd",
        "resolution": 1,
        "summaryScoreMode": "whiskers",
        "filled": false,
        "scaleType": "linear",
        "displayCrossHatches": false,
        "configuration": "merlin.bw_1-LinearWiggleDisplay"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "test-6.bed_2",
      "name": "test-6.bed_2",
      "assemblyNames": [
        "Merlin"
      ],
      "adapter": {
        "category": [
          "Assembly properties"
        ],
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "test-6.bed_2.gz",
          "columnNames": [
            "chr",
            "start",
            "end",
            "name",
            "score"
          ],
          "scoreColumn": "score"
        },
        "index": {
          "location": {
            "uri": "test-6.bed_2.gz.tbi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "test-6.bed_2-LinearBasicDisplay",
          "renderer": {
            "type": "SvgFeatureRenderer",
            "color1": "jexl:customColor(feature)"
          }
        },
        {
          "type": "LinearPileupDisplay",
          "displayId": "test-6.bed_2-LinearPileupDisplay"
        },
        {
          "type": "LinearArcDisplay",
          "displayId": "test-6.bed_2-LinearArcDisplay"
        }
      ],
      "style": {
        "type": "LinearBasicDisplay",
        "displayId": "test-6.bed_2-LinearBasicDisplay",
        "trackShowLabels": false,
        "trackShowDescriptions": false,
        "configuration": "test-6.bed_2-LinearBasicDisplay"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "merlin.vcf_3",
      "name": "merlin.vcf_3",
      "assemblyNames": [
        "Merlin"
      ],
      "category": [
        "Assembly properties"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "merlin.vcf_3"
        },
        "index": {
          "location": {
            "uri": "merlin.vcf_3.tbi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearVariantDisplay",
          "displayId": "merlin.vcf_3-LinearVariantDisplay"
        },
        {
          "type": "ChordVariantDisplay",
          "displayId": "merlin.vcf_3-ChordVariantDisplay"
        },
        {
          "type": "LinearPairedArcDisplay",
          "displayId": "merlin.vcf_3-LinearPairedArcDisplay"
        }
      ],
      "style": {
        "type": "LinearVariantDisplay",
        "displayId": "merlin.vcf_3-LinearVariantDisplay",
        "trackShowLabels": false,
        "trackShowDescriptions": false,
        "configuration": "merlin.vcf_3-LinearVariantDisplay"
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "merlin.cram_4",
      "name": "merlin.cram_4",
      "category": [
        "Assembly properties"
      ],
      "assemblyNames": [
        "Merlin"
      ],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "merlin.cram_4"
        },
        "craiLocation": {
          "uri": "merlin.cram_4.crai"
        },
        "sequenceAdapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "Merlin.fa.gz"
          },
          "faiLocation": {
            "uri": "Merlin.fa.gz.fai"
          },
          "gziLocation": {
            "uri": "Merlin.fa.gz.gzi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearAlignmentsDisplay",
          "displayId": "merlin.cram_4-LinearAlignmentsDisplay"
        }
      ],
      "style": {
        "type": "LinearAlignmentsDisplay",
        "displayId": "merlin.cram_4-LinearAlignmentsDisplay",
        "configuration": "merlin.cram_4-LinearAlignmentsDisplay"
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "merlin-sample.bam_5",
      "name": "merlin-sample.bam_5",
      "category": [
        "Assembly properties"
      ],
      "assemblyNames": [
        "Merlin"
      ],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "merlin-sample.bam_5"
        },
        "index": {
          "location": {
            "uri": "merlin-sample.bam_5.bai"
          }
        }
      },
      "displays": [
        {
          "type": "LinearAlignmentsDisplay",
          "displayId": "merlin-sample.bam_5-LinearAlignmentsDisplay"
        }
      ],
      "style": {
        "type": "LinearAlignmentsDisplay",
        "displayId": "merlin-sample.bam_5-LinearAlignmentsDisplay",
        "configuration": "merlin-sample.bam_5-LinearAlignmentsDisplay"
      }
    },
    {
      "type": "MafTrack",
      "trackId": "merlinlastz.maf_6",
      "name": "merlinlastz.maf_6",
      "category": [
        "Assembly properties"
      ],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": [
          "Merlin",
          "Merlin1",
          "Merlin2",
          "Merlin3",
          "Merlin4",
          "Merlin5",
          "Merlin6"
        ],
        "bedGzLocation": {
          "uri": "merlinlastz.maf_6.sorted.bed.gz"
        },
        "index": {
          "location": {
            "uri": "merlinlastz.maf_6.sorted.bed.gz.tbi"
          }
        }
      },
      "assemblyNames": [
        "Merlin"
      ],
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "merlinlastz.maf_6-LinearBasicDisplay"
        },
        {
          "type": "LinearArcDisplay",
          "displayId": "merlinlastz.maf_6-LinearArcDisplay"
        }
      ],
      "style": {
        "type": "LinearBasicDisplay",
        "displayId": "merlinlastz.maf_6-LinearBasicDisplay",
        "trackShowLabels": false,
        "trackShowDescriptions": false,
        "configuration": "merlinlastz.maf_6-LinearBasicDisplay"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "merlin.blastxml_7",
      "name": "merlin.blastxml_7",
      "assemblyNames": [
        "Merlin"
      ],
      "category": [
        "Assembly properties"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "merlin.blastxml_7.gz"
        },
        "index": {
          "location": {
            "uri": "merlin.blastxml_7.gz.tbi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "merlin.blastxml_7-LinearBasicDisplay"
        },
        {
          "type": "LinearArcDisplay",
          "displayId": "merlin.blastxml_7-LinearArcDisplay"
        }
      ],
      "style": {
        "type": "LinearBasicDisplay",
        "displayId": "merlin.blastxml_7-LinearBasicDisplay",
        "trackShowLabels": false,
        "trackShowDescriptions": false,
        "configuration": "merlin.blastxml_7-LinearBasicDisplay"
      }
    },
    {
      "type": "HicTrack",
      "trackId": "dm3test.cool_9",
      "name": "dm3test.cool_9",
      "assemblyNames": [
        "dm3.fa"
      ],
      "displays": [
        {
          "type": "LinearHicDisplay",
          "displayId": "dm3test.cool_9-LinearHicDisplay"
        }
      ],
      "category": [
        "Assembly properties"
      ],
      "adapter": {
        "type": "HicAdapter",
        "hicLocation": {
          "uri": "dm3test.cool_9.hic"
        }
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "peach-grape-map.paf_10",
      "assemblyNames": [
        "Ppersica1.fa",
        "Vvinifera1.fa"
      ],
      "category": [
        "Assembly properties"
      ],
      "name": "peach-grape-map.paf_10",
      "displays": [
        {
          "type": "LGVSyntenyDisplay",
          "displayId": "peach-grape-map.paf_10-LGVSyntenyDisplay"
        },
        {
          "type": "DotplotDisplay",
          "displayId": "peach-grape-map.paf_10-DotplotDisplay"
        },
        {
          "type": "LinearComparativeDisplay",
          "displayId": "peach-grape-map.paf_10-LinearComparativeDisplay"
        },
        {
          "type": "LinearBasicDisplay",
          "displayId": "peach-grape-map.paf_10-LinearSyntenyDisplay"
        }
      ],
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "pifGzLocation": {
          "uri": "peach-grape-map.paf_10"
        },
        "assemblyNames": [
          "Ppersica1.fa",
          "Vvinifera1.fa"
        ],
        "index": {
          "location": {
            "uri": "peach-grape-map.paf_10.tbi"
          }
        }
      },
      "style": {
        "type": "LGVSyntenyDisplay",
        "displayId": "peach-grape-map.paf_10-LinearBasicDisplay",
        "configuration": "peach-grape-map.paf_10-LGVSyntenyDisplay"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "arabgrapepeach.paf_11",
      "assemblyNames": [
        "Ppersica1.fa",
        "arabidopsis.URI",
        "Vvinifera1.URI"
      ],
      "category": [
        "Assembly properties"
      ],
      "name": "arabgrapepeach.paf_11",
      "displays": [
        {
          "type": "LGVSyntenyDisplay",
          "displayId": "arabgrapepeach.paf_11-LGVSyntenyDisplay"
        },
        {
          "type": "DotplotDisplay",
          "displayId": "arabgrapepeach.paf_11-DotplotDisplay"
        },
        {
          "type": "LinearComparativeDisplay",
          "displayId": "arabgrapepeach.paf_11-LinearComparativeDisplay"
        },
        {
          "type": "LinearBasicDisplay",
          "displayId": "arabgrapepeach.paf_11-LinearSyntenyDisplay"
        }
      ],
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "pifGzLocation": {
          "uri": "arabgrapepeach.paf_11"
        },
        "assemblyNames": [
          "Ppersica1.fa",
          "arabidopsis.URI",
          "Vvinifera1.URI"
        ],
        "index": {
          "location": {
            "uri": "arabgrapepeach.paf_11.tbi"
          }
        }
      },
      "style": {
        "type": "LGVSyntenyDisplay",
        "displayId": "arabgrapepeach.paf_11-LinearBasicDisplay",
        "configuration": "arabgrapepeach.paf_11-LGVSyntenyDisplay"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "arabgrapepeach.paf_12",
      "assemblyNames": [
        "Ppersica1.fa",
        "Vvinifera1.fa"
      ],
      "category": [
        "Assembly properties"
      ],
      "name": "arabgrapepeach.paf_12",
      "displays": [
        {
          "type": "LGVSyntenyDisplay",
          "displayId": "arabgrapepeach.paf_12-LGVSyntenyDisplay"
        },
        {
          "type": "DotplotDisplay",
          "displayId": "arabgrapepeach.paf_12-DotplotDisplay"
        },
        {
          "type": "LinearComparativeDisplay",
          "displayId": "arabgrapepeach.paf_12-LinearComparativeDisplay"
        },
        {
          "type": "LinearBasicDisplay",
          "displayId": "arabgrapepeach.paf_12-LinearSyntenyDisplay"
        }
      ],
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "pifGzLocation": {
          "uri": "arabgrapepeach.paf_12"
        },
        "assemblyNames": [
          "Ppersica1.fa",
          "Vvinifera1.fa"
        ],
        "index": {
          "location": {
            "uri": "arabgrapepeach.paf_12.tbi"
          }
        }
      },
      "style": {
        "type": "LGVSyntenyDisplay",
        "displayId": "arabgrapepeach.paf_12-LinearBasicDisplay",
        "configuration": "arabgrapepeach.paf_12-LGVSyntenyDisplay"
      }
    },
    {
      "type": "HicTrack",
      "trackId": "humanhic_13",
      "name": "humanhic_13",
      "assemblyNames": [
        "hg38"
      ],
      "displays": [
        {
          "type": "LinearHicDisplay",
          "displayId": "humanhic_13-LinearHicDisplay"
        }
      ],
      "category": [
        "Assembly properties"
      ],
      "adapter": {
        "type": "HicAdapter",
        "hicLocation": {
          "uri": "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"
        }
      }
    }
  ],
  "assemblies": [
    {
      "name": "Merlin",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Merlin",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "Merlin.fa.gz"
          },
          "faiLocation": {
            "uri": "Merlin.fa.gz.fai"
          },
          "gziLocation": {
            "uri": "Merlin.fa.gz.gzi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearReferenceSequenceDisplay",
          "displayId": "Merlin-LinearReferenceSequenceDisplay"
        },
        {
          "type": "LinearGCContentDisplay",
          "displayId": "Merlin-LinearGCContentDisplay"
        }
      ]
    },
    {
      "name": "dm3.fa",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "dm3.fa",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "dm3.fa.fa.gz"
          },
          "faiLocation": {
            "uri": "dm3.fa.fa.gz.fai"
          },
          "gziLocation": {
            "uri": "dm3.fa.fa.gz.gzi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearReferenceSequenceDisplay",
          "displayId": "dm3.fa-LinearReferenceSequenceDisplay"
        },
        {
          "type": "LinearGCContentDisplay",
          "displayId": "dm3.fa-LinearGCContentDisplay"
        }
      ]
    },
    {
      "name": "Ppersica1.fa",
      "sequence": {
        "type": "ReferenceSequenceTrack",
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