tooluniverse-data-wrangling
Data Wrangling: Universal Access Patterns
Reference for downloading and parsing scientific data from any source. Write and run Python code via Bash for every step.
When to Use
- ToolUniverse tool returned metadata/search results but you need raw or bulk data
- Data is in a format tools don't parse (VCF, h5ad, BAM, SDF, GCT)
- You need a multi-step API workflow (search -> filter -> download -> parse)
- The data source has no ToolUniverse tool at all
- You need thousands of records, not the 10-100 a tool returns
Decision: Tool vs Code
| Situation | Use |
|---|---|
| Single record lookup, simple search, <100 results | ToolUniverse tool (execute_tool) |
| Bulk download, custom filtering, format conversion | Write Python code |
| Tool exists but returns truncated results | Write code using the same API the tool wraps |
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