bedtools/bedtools_links
HTML
Links
UCSC
Browser
BED
GFF
VCF
Description
This tool generates an HTML page containing links to the UCSC Genome Browser
for each feature/interval in the input file. This is particularly useful for
manually inspecting large sets of genomic annotations or features through
the browser interface.
Default behavior: Links point to human genome (hg18) on the main UCSC site
Customization: Supports custom mirror sites and different organisms/builds
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input file in BED, GFF, or VCF format containing genomic intervals. Each feature/interval will be converted to a clickable link pointing to the UCSC Genome Browser. File format is auto-detected based on content and extension. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output HTML file containing clickable browser links. The generated HTML page will contain one link per input feature, formatted for easy navigation to the UCSC Genome Browser. |
Options
Name | Type & Properties | Description |
|---|---|---|
--base_url -base | string | Base URL for the UCSC Genome Browser instance. **Default:** http://genome.ucsc.edu (official UCSC site) **Custom mirrors:** Use your institution's mirror URL **Example:** http://mymirror.myuniversity.edu |
--organism -org | string | Target organism for genome browser links. **Common values:** - human (default) - mouse - rat - fly - worm Must match organism names used by your UCSC browser instance. |
--database -db | string | Genome assembly/build identifier. **Human examples:** hg19, hg38, hg18 (default) **Mouse examples:** mm9, mm10, mm39 **Other:** Assembly names as recognized by UCSC browser Must correspond to available assemblies for the specified organism. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.html"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.1 \
-main-script target/nextflow/bedtools/bedtools_links/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_linksbiobox v0.4.1
Uses
0 relationships
No component dependencies found.