@galaxyproject/igv 0.0.0 → 0.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
package/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2024
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
package/README.md ADDED
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+ # Galaxy Charts Starter Kit
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+
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+ This template repository provides a quick start for developing visualizations within the Galaxy platform.
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+
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+ [Click here to learn more.](https://galaxyproject.github.io/galaxy-charts/)
package/package.json CHANGED
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  {
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  "name": "@galaxyproject/igv",
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- "version": "0.0.0",
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+ "version": "0.0.1",
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  "type": "module",
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+ "license": "MIT",
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  "files": [
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- "static/dist/index.js",
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- "static/dist/index.css"
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+ "static"
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  ],
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  "scripts": {
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  "dev": "vite",
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  "build": "vite build",
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  "preview": "vite preview",
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- "prettier": "prettier --write 'package.json' 'src/**/*.js'"
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+ "prettier": "prettier --config ./prettier.config.js --write './*.{js,ts,json}' 'src/**/*.{js,ts,json,css,vue}'",
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+ "test": "vitest",
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+ "test:watch": "vitest --watch",
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+ "test:ui": "vitest --ui"
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  },
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  "devDependencies": {
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- "axios": "^1.8.4",
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- "igv": "^3.2.5",
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- "prettier": "^3.4.1",
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- "vite": "^6.2.0"
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+ "@types/node": "^22.9.0",
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+ "@vitejs/plugin-vue": "^5.0.5",
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+ "@vitest/ui": "^3.0.9",
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+ "autoprefixer": "^10.4.19",
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+ "galaxy-charts": "^0.0.75",
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+ "galaxy-charts-xml-parser": "^1.0.3",
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+ "igv": "^3.5.0",
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+ "jsdom": "^25.0.1",
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+ "postcss": "^8.4.40",
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+ "prettier": "^3.3.3",
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+ "tailwindcss": "^3.4.7",
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+ "typescript": "^5.5.4",
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+ "vite": "^6.2.2",
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+ "vitest": "^3.0.9",
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+ "vue": "^3.4.31",
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+ "yaml": "^2.8.1"
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  }
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  }
package/static/igv.xml ADDED
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
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+ <visualization name="IGV">
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+ <description>Interactive Genome Visualization</description>
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+ <data_sources>
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+ <data_source>
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+ <model_class>HistoryDatasetAssociation</model_class>
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+ <test test_attr="ext">2bit</test>
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+ <test test_attr="ext">bam</test>
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+ <test test_attr="ext">bcf</test>
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+ <test test_attr="ext">bed</test>
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+ <test test_attr="ext">bedgraph</test>
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+ <test test_attr="ext">bigbed</test>
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+ <test test_attr="ext">bigwig</test>
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+ <test test_attr="ext">broadpeak</test>
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+ <test test_attr="ext">bw</test>
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+ <test test_attr="ext">cram</test>
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+ <test test_attr="ext">fa</test>
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+ <test test_attr="ext">fasta</test>
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+ <test test_attr="ext">gff</test>
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+ <test test_attr="ext">gff3</test>
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+ <test test_attr="ext">gtf</test>
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+ <test test_attr="ext">narrowpeak</test>
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+ <test test_attr="ext">vcf</test>
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+ <test test_attr="ext">vcf_bgzip</test>
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+ <test test_attr="ext">wig</test>
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+ </data_source>
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+ </data_sources>
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+ <params>
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+ <param required="true">dataset_id</param>
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+ </params>
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+ <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
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+ <settings>
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+ <input>
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+ <label>Genome</label>
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+ <help>Select a reference genome supported by igv.js</help>
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+ <name>genome</name>
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+ <type>select</type>
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+ <filterable>true</filterable>
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+ <value>hg38</value>
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+ <data>
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+ <data><label>Human (T2T CHM13-v2.0/hs1)</label><value>hs1</value></data>
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+ <data><label>Human (T2T CHM13-v1.1)</label><value>chm13v1.1</value></data>
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+ <data><label>Human (GRCh38/hg38)</label><value>hg38</value></data>
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+ <data><label>Human (hg38 1kg/GATK)</label><value>hg38_1kg</value></data>
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+ <data><label>Human (GRCh37/hg19)</label><value>hg19</value></data>
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+ <data><label>Human (hg18)</label><value>hg18</value></data>
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+ <data><label>Mouse (GRCm39/mm39)</label><value>mm39</value></data>
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+ <data><label>Mouse (GRCm38/mm10)</label><value>mm10</value></data>
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+ <data><label>Mouse (NCBI37/mm9)</label><value>mm9</value></data>
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+ <data><label>Rat (rn7)</label><value>rn7</value></data>
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+ <data><label>Rat (RGCS 6.0/rn6)</label><value>rn6</value></data>
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+ <data><label>Gorilla (Kamilah_GGO_v0/gorGor6)</label><value>gorGor6</value></data>
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+ <data><label>Gorilla (gorGor4.1/gorGor4)</label><value>gorGor4</value></data>
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+ <data><label>Chimp (panTro6)</label><value>panTro6</value></data>
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+ <data><label>Chimp (panTro5)</label><value>panTro5</value></data>
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+ <data><label>Chimp (SAC 2.1.4/panTro4)</label><value>panTro4</value></data>
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+ <data><label>Macaca fascicularis (macFas5)</label><value>macFas5</value></data>
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+ <data><label>Macaca fascicularis 6.0 (GCA_011100615.1)</label><value>GCA_011100615.1</value></data>
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+ <data><label>Bonobo (MPI-EVA panpan1.1/panPan2)</label><value>panPan2</value></data>
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+ <data><label>Dog (Broad CanFam3.1/canFam3)</label><value>canFam3</value></data>
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+ <data><label>Dog (UU_Cfam_GSD_1.0/canFam4)</label><value>canFam4</value></data>
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+ <data><label>Dog (canFam5)</label><value>canFam5</value></data>
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+ <data><label>Cow (ARS-UCD1.2/bosTau9)</label><value>bosTau9</value></data>
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+ <data><label>Cow (UMD_3.1.1/bosTau8)</label><value>bosTau8</value></data>
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+ <data><label>Pig (SGSC Sscrofa11.1/susScr11)</label><value>susScr11</value></data>
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+ <data><label>Chicken (galGal6)</label><value>galGal6</value></data>
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+ <data><label>Gallus gallus (GCF_016699485.2)</label><value>GCF_016699485.2</value></data>
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+ <data><label>Zebrafish (GRCZ11/danRer11)</label><value>danRer11</value></data>
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+ <data><label>Zebrafish (GRCZ10/danRer10)</label><value>danRer10</value></data>
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+ <data><label>C. elegans (ce11)</label><value>ce11</value></data>
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+ <data><label>D. melanogaster (dm6)</label><value>dm6</value></data>
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+ <data><label>D. melanogaster (dm3)</label><value>dm3</value></data>
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+ <data><label>D. melanogaster (dmel_r5.9)</label><value>dmel_r5.9</value></data>
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+ <data><label>S. cerevisiae (sacCer3)</label><value>sacCer3</value></data>
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+ <data><label>S. pombe (ASM294v2)</label><value>ASM294v2</value></data>
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+ <data><label>Sars-CoV-2 (ASM985889v3)</label><value>ASM985889v3</value></data>
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+ <data><label>A. thaliana (TAIR 10)</label><value>tair10</value></data>
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+ <data><label>Peanut (GCA_003086295.2)</label><value>GCA_003086295.2</value></data>
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+ <data><label>O. sativa IRGSP-1.0 (GCF_001433935.1)</label><value>GCF_001433935.1</value></data>
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+ <data><label>Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S</label><value>NC_016856.1</value></data>
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+ <data><label>Coprinopsis cinerea okayama7#130 (GCA_000182895.1)</label><value>GCA_000182895.1</value></data>
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+ </data>
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+ </input>
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+ <input>
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+ <label>Locus</label>
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+ <help>Select a gene locus e.g. chr1:1-100</help>
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+ <name>locus</name>
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+ <type>text</type>
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+ <value>all</value>
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+ </input>
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+ </settings>
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+ <tracks>
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+ <input>
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+ <label>Name</label>
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+ <help>Specify a name</help>
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+ <name>name</name>
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+ <type>text</type>
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+ <value>Track</value>
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+ </input>
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+ <input>
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+ <label>Dataset</label>
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+ <help>Specify a dataset</help>
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+ <name>urlDataset</name>
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+ <type>data</type>
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+ </input>
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+ <input>
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+ <label>Index</label>
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+ <help>Specify an index</help>
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+ <name>indexUrlDataset</name>
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+ <type>data</type>
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+ <optional>true</optional>
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+ </input>
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+ <input>
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+ <label>Type</label>
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+ <help>Select the track type (only if not auto-detected from file format)</help>
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+ <name>type</name>
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+ <type>select</type>
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+ <value>auto</value>
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+ <data>
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+ <data><label>Auto</label><value>auto</value></data>
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+ <data><label>Annotation</label><value>annotation</value></data>
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+ <data><label>Copy Number Variation (CNV)</label><value>cnv</value></data>
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+ <data><label>SNP</label><value>snp</value></data>
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+ <data><label>GA4GH</label><value>ga4gh</value></data>
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+ </data>
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+ </input>
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+ <input>
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+ <label>Mode</label>
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+ <help>Select a display mode</help>
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+ <name>displayMode</name>
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+ <type>select</type>
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+ <value>EXPANDED</value>
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+ <data>
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+ <data><label>Collapsed</label><value>COLLAPSED</value></data>
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+ <data><label>Squished</label><value>SQUISHED</value></data>
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+ <data><label>Expanded</label><value>EXPANDED</value></data>
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+ </data>
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+ </input>
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+ <input>
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+ <label>Color</label>
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+ <help>Pick a color</help>
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+ <name>color</name>
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+ <type>color</type>
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+ </input>
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+ </tracks>
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+ </visualization>
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+ <!doctype html>
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+ <html lang="en">
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+ <head>
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+ <meta charset="UTF-8" />
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+ <link rel="icon" href="charts.svg" sizes="any" type="image/svg+xml" />
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+ <title>Galaxy Charts</title>
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+ <script type="module" crossorigin src="/index.js"></script>
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+ <link rel="stylesheet" crossorigin href="/index.css">
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+ </head>
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+ <body>
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+ <div id="custom"></div>
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+ </body>
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+ </html>