diff test-data/out/02_remote/config.json @ 0:61add3f58f26 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
author iuc
date Thu, 02 Oct 2025 10:19:44 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out/02_remote/config.json	Thu Oct 02 10:19:44 2025 +0000
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+{
+  "assemblies": [
+    {
+      "name": "hg19",
+      "sequence": {
+        "type": "ReferenceSequenceTrack",
+        "trackId": "hg19-ReferenceSequenceTrack",
+        "adapter": {
+          "type": "BgzipFastaAdapter",
+          "fastaLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
+            "locationType": "UriLocation"
+          },
+          "faiLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
+            "locationType": "UriLocation"
+          },
+          "gziLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    }
+  ],
+  "configuration": {
+    "disableAnalytics": false,
+    "theme": {
+      "palette": {
+        "primary": {
+          "main": "#0d233f"
+        },
+        "secondary": {
+          "main": "#721e63"
+        },
+        "tertiary": {
+          "main": "#135560"
+        },
+        "quaternary": {
+          "main": "#ffb11d"
+        }
+      },
+      "typography": {
+        "fontSize": 10
+      }
+    }
+  },
+  "connections": [],
+  "defaultSession": {
+    "name": "hg19",
+    "views": [
+      {
+        "type": "LinearGenomeView",
+        "init": {
+          "assembly": "hg19",
+          "loc": "1",
+          "tracks": [
+            "f25077b166d61daa5cd442a5341a6778_0_0",
+            "d356ba515264f7745079b8a8e25265e0_1_0",
+            "4c55c087663d6bbdba9c10dba1371ef7_2_0",
+            "0679f3e546fddf3021cce6cc4cdc5683_3_0",
+            "717916f48c0481fcd916da20c9db8f3d_4_0",
+            "b7b77cd71a6754bae52b38ac1bfcb1df_5_0",
+            "d1c14592b12aa3d38a8c9114afb34f7d_6_0",
+            "b99150c19ec943d2d90eeab328e8ac4e_7_0",
+            "0e1a5cd1079b0cc284247c45ab58e154_8_0"
+          ]
+        }
+      }
+    ]
+  },
+  "tracks": [
+    {
+      "type": "QuantitativeTrack",
+      "trackId": "f25077b166d61daa5cd442a5341a6778_0_0",
+      "name": "SKBR3 pacbio coverage (NGMLR)",
+      "adapter": {
+        "type": "BigWigAdapter",
+        "bigWigLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw",
+          "locationType": "UriLocation"
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "LinearWiggleDisplay",
+          "displayId": "f25077b166d61daa5cd442a5341a6778_0_0_LinearWiggleDisplay",
+          "defaultRendering": "xyplot"
+        }
+      ],
+      "metadata": {}
+    },
+    {
+      "type": "MultiQuantitativeTrack",
+      "trackId": "d356ba515264f7745079b8a8e25265e0_1_0",
+      "name": "SKBR3 pacbio coverage (NGMLR) + 0 other track",
+      "adapter": {
+        "type": "MultiWiggleAdapter",
+        "subadapters": [
+          {
+            "type": "BigWigAdapter",
+            "name": "SKBR3 pacbio coverage (NGMLR)",
+            "bigWigLocation": {
+              "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw",
+              "locationType": "UriLocation"
+            }
+          }
+        ]
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "MultiLinearWiggleDisplay",
+          "displayId": "d356ba515264f7745079b8a8e25265e0_1_0_MultiLinearWiggleDisplay",
+          "defaultRendering": "multirowxy"
+        }
+      ],
+      "metadata": {}
+    },
+    {
+      "type": "AlignmentsTrack",
+      "trackId": "4c55c087663d6bbdba9c10dba1371ef7_2_0",
+      "name": "NA12878 Exome",
+      "adapter": {
+        "type": "BamAdapter",
+        "bamLocation": {
+          "uri": "https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.bai",
+            "locationType": "UriLocation"
+          },
+          "indexType": "BAI"
+        },
+        "sequenceAdapter": {
+          "type": "BgzipFastaAdapter",
+          "fastaLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
+            "locationType": "UriLocation"
+          },
+          "faiLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
+            "locationType": "UriLocation"
+          },
+          "gziLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
+            "locationType": "UriLocation"
+          }
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "LinearAlignmentsDisplay",
+          "displayId": "4c55c087663d6bbdba9c10dba1371ef7_2_0_LinearAlignmentsDisplay"
+        }
+      ],
+      "metadata": {}
+    },
+    {
+      "type": "AlignmentsTrack",
+      "trackId": "0679f3e546fddf3021cce6cc4cdc5683_3_0",
+      "name": "hg_isoforms.fasta_cram",
+      "adapter": {
+        "type": "CramAdapter",
+        "cramLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram",
+          "locationType": "UriLocation"
+        },
+        "craiLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram.crai",
+          "locationType": "UriLocation"
+        },
+        "sequenceAdapter": {
+          "type": "BgzipFastaAdapter",
+          "fastaLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
+            "locationType": "UriLocation"
+          },
+          "faiLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
+            "locationType": "UriLocation"
+          },
+          "gziLocation": {
+            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
+            "locationType": "UriLocation"
+          }
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "LinearAlignmentsDisplay",
+          "displayId": "0679f3e546fddf3021cce6cc4cdc5683_3_0_LinearAlignmentsDisplay"
+        }
+      ],
+      "metadata": {}
+    },
+    {
+      "type": "HicTrack",
+      "trackId": "717916f48c0481fcd916da20c9db8f3d_4_0",
+      "name": "hg_isoforms.fasta_cram",
+      "adapter": {
+        "type": "HicAdapter",
+        "hicLocation": {
+          "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic",
+          "locationType": "UriLocation"
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "LinearHicDisplay",
+          "displayId": "717916f48c0481fcd916da20c9db8f3d_4_0_LinearHicDisplay"
+        }
+      ],
+      "metadata": {}
+    },
+    {
+      "type": "VariantTrack",
+      "trackId": "b7b77cd71a6754bae52b38ac1bfcb1df_5_0",
+      "name": "HG002 dbVar variant calls",
+      "adapter": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "LinearVariantDisplay",
+          "displayId": "b7b77cd71a6754bae52b38ac1bfcb1df_5_0_LinearVariantDisplay"
+        }
+      ],
+      "formatDetails": {},
+      "metadata": {}
+    },
+    {
+      "type": "VariantTrack",
+      "trackId": "d1c14592b12aa3d38a8c9114afb34f7d_6_0",
+      "name": "truthset_somaticSVs_COLO829",
+      "adapter": {
+        "type": "VcfAdapter",
+        "vcfLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/COLO829/truthset_somaticSVs_COLO829.vcf",
+          "locationType": "UriLocation"
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "LinearVariantDisplay",
+          "displayId": "d1c14592b12aa3d38a8c9114afb34f7d_6_0_LinearVariantDisplay"
+        }
+      ],
+      "formatDetails": {},
+      "metadata": {}
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "b99150c19ec943d2d90eeab328e8ac4e_7_0",
+      "name": "Gencode v36 (GRCh37 liftover)",
+      "adapter": {
+        "type": "Gff3TabixAdapter",
+        "gffGzLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "LinearBasicDisplay",
+          "displayId": "b99150c19ec943d2d90eeab328e8ac4e_7_0_LinearBasicDisplay",
+          "renderer": {
+            "type": "SvgFeatureRenderer",
+            "showLabels": true,
+            "showDescriptions": true,
+            "labels": {
+              "name": "jexl:get(feature,'name') || get(feature,'id')",
+              "description": "jexl:get(feature,'note') || get(feature,'description')"
+            },
+            "displayMode": "normal",
+            "maxHeight": 600
+          }
+        }
+      ],
+      "formatDetails": {
+        "depth": 1
+      },
+      "metadata": {}
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "0e1a5cd1079b0cc284247c45ab58e154_8_0",
+      "name": "wgEncodeDukeMapabilityRegionsExcludable",
+      "adapter": {
+        "type": "BedTabixAdapter",
+        "bedGzLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
+        }
+      },
+      "category": [
+        "Default"
+      ],
+      "assemblyNames": [
+        "hg19"
+      ],
+      "displays": [
+        {
+          "type": "LinearBasicDisplay",
+          "displayId": "0e1a5cd1079b0cc284247c45ab58e154_8_0_LinearBasicDisplay",
+          "renderer": {
+            "type": "SvgFeatureRenderer",
+            "showLabels": true,
+            "showDescriptions": true,
+            "labels": {
+              "name": "jexl:get(feature,'name') || get(feature,'id')",
+              "description": "jexl:get(feature,'note') || get(feature,'description')"
+            },
+            "displayMode": "normal",
+            "maxHeight": 600
+          }
+        }
+      ],
+      "formatDetails": {
+        "depth": 1
+      },
+      "metadata": {}
+    }
+  ],
+  "plugins": []
+}
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