@galaxyproject/igv 0.0.4 → 0.0.7
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/package.json +2 -2
- package/static/igv.xml +63 -54
- package/static/index.css +1 -1
- package/static/index.js +249 -249
package/package.json
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{
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"name": "@galaxyproject/igv",
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"version": "0.0.
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"version": "0.0.7",
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"type": "module",
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"license": "MIT",
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"files": [
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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.
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"galaxy-charts": "^0.0.81",
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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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package/static/igv.xml
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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">
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<test test_attr="ext">twobit</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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<entry_point entry_point_type="script" src="index.js" css="index.css" />
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<settings>
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<input>
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<label>
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<help>
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<name>
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<type>
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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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<label>Source</label>
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<help>Switch to genomes provided IGV</help>
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<name>source</name>
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<type>conditional</type>
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<test_param>
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<name>from_igv</name>
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<type>boolean</type>
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<value>false</value>
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</test_param>
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<cases>
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<cases>
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<value>false</value>
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<inputs>
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<inputs>
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<label>Genome</label>
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<help>Select a reference genome</help>
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<name>genome</name>
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<type>data_table</type>
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<tables>
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<tables>fasta_indexes</tables>
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<tables>twobit</tables>
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</tables>
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</inputs>
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</inputs>
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</cases>
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<cases>
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<value>true</value>
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<inputs>
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<inputs>
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<label>Genome</label>
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<help>Select a reference genome provided by IGV</help>
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<name>genome</name>
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<type>data_json</type>
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<url>https://s3.amazonaws.com/igv.org.genomes/genomes.json</url>
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</inputs>
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</inputs>
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</cases>
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</cases>
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</input>
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<input>
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<label>Locus</label>
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<type>color</type>
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</input>
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</tracks>
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<tests>
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<test>
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<param name="dataset_id" value="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/gencode.v29.annotation.bed" ftype="bed" />
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</test>
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<test>
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<param name="dataset_id" value="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/gencode.v29.annotation.gff3" ftype="gff3" />
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</test>
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</tests>
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<help format="markdown"><![CDATA[
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# What is IGV?
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The Integrative Genomics Viewer (IGV) is a high-performance, interactive browser for exploring large genomic datasets. This tool integrates seamlessly with Galaxy to provide fast, scalable visualization of sequencing data and annotations directly in the browser.
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## Key Features
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- **Multi-format Support*: View alignments, variants, annotations, and coverage from BAM, CRAM, VCF, GFF/GTF, BED, BigWig, BigBed, and more.
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- **Reference Genomes**: Load locally indexed FASTA/2bit references or select from IGV’s extensive genome collection.
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- **Interactive Navigation**: Jump to specific chromosomes, loci, or genes; zoom across whole chromosomes or individual bases.
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- **Track Management**: Add multiple datasets as tracks, configure colors, display modes, and track types.
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- **Scalability**: Optimized for very large datasets with smooth, real-time panning and zooming.
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- **Custom Views**: Adjust track layouts, collapse or expand features, and highlight regions of interest.
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Learn more at: https://igv.org
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]]></help>
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</visualization>
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package/static/index.css
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html,:host{line-height:1.5;-webkit-text-size-adjust:100%;-moz-tab-size:4;-o-tab-size:4;tab-size:4;font-family:ui-sans-serif,system-ui,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol,"Noto Color Emoji";font-feature-settings:normal;font-variation-settings:normal;-webkit-tap-highlight-color:transparent}code,kbd,samp,pre{font-family:ui-monospace,SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,monospace;font-feature-settings:normal;font-variation-settings:normal;font-size:1em}.visible{visibility:visible}.absolute{position:absolute}.relative{position:relative}.right-0{right:0}.z-10{z-index:10}.z-\[1\]{z-index:1}.m-2{margin:.5rem}.mx-1{margin-left:.25rem;margin-right:.25rem}.mx-2{margin-left:.5rem;margin-right:.5rem}.my-1{margin-top:.25rem;margin-bottom:.25rem}.my-2{margin-top:.5rem;margin-bottom:.5rem}.mb-1{margin-bottom:.25rem}.mb-2{margin-bottom:.5rem}.mr-1{margin-right:.25rem}.mr-2{margin-right:.5rem}.mt-
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