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

Type

bash_script

License

MIT

Keywords

HTML

Links

UCSC

Browser

BED

GFF

VCF

Links

Repository

Documentation

Contributors

Launch

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

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.

Name

Type & Properties

--input

-i

file

required

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.

Name

Type & Properties

--output

-o

file

required

output

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.

Name

Type & Properties

--base_url

-base

string

--organism

-org

string

--database

-db

string