xt

CLI for Xiantao bioinformatics tools.

Install with npm i -g @helixlife-ai/xiantao and run it as xt.

tool is the primary product topic for bioinformatics tools. plot is kept as a compatibility entrypoint for the current command set and prints a migration warning when executed.

--profile is the primary profile selector for token lookup and config isolation. If it is omitted, the CLI resolves the profile from AGENT_NAME, then the host runtime (cursor, opencode, openclaw), then ~/.config/xtz/config.json, and finally defaults to opencode. --agent is kept as a compatibility alias.

login, status, and logout are the primary auth entrypoints. auth ... is kept as a compatibility topic and prints a migration warning when executed.

Main Flows

First Use

xt login
xt tool search violin
xt tool inspect violin_flat
xt tool run violin_flat ./data.xlsx

xt login is the recommended first-use entrypoint. It refreshes both the upload token and the Xiantao web token for the current profile. xt tool login is kept as an equivalent entrypoint under the tool topic.

Interactive Tool Run

xt tool run --interactive

This starts a menu-driven path for choosing a tool, selecting demo data or a local file, filling dynamic args_main, and optionally downloading generated outputs.

Agent Automation

xt tool exec violin_flat --file ./data.xlsx --profile opencode --json

For machine callers, use xt tool exec, keep --json, pass an explicit profile with --profile, and avoid interactive-only flows.

Command Groups

Auth

• xt login
• xt status
• xt logout
• xt tool login

Tool Run

• xt tool search
• xt tool inspect
• xt tool run
• xt tool exec
• xt tool download

Tool Debug

• xt tool resolve
• xt tool menu
• xt tool menus
• xt tool fetch-all

Notes

For the common Xiantao tool product, tool search, tool inspect, tool run, tool resolve, and tool menu default toolProductUuid to c0b6febb-52dd-4525-970a-61bbe9e263ff. You can override it with --toolProductUuid, XIANTAO_TOOL_PRODUCT_UUID, or ~/.config/xtz/config.json under xiantao.toolProductUuid.

xt tool search <keyword> searches cached or remote tool menus by tool id, title, path, and route. xt tool inspect <tool_id> prints resolved metadata together with the dynamic args_main schema used by the tool. xt tool run <tool_id> runs a Xiantao bioinformatics tool. xt tool resolve <tool_id> remains available as the low-level UUID and route lookup. --demo reuses the demo file metadata returned by tool fetch-all; otherwise tool run uploads the local file first and therefore also needs upload auth. Run xt login first to refresh both tokens in one step. When a tool exposes multiple downloadable results, --download <path> uses the output file extension to select the matching artifact.

xt tool run <tool_id> ... --interactive prompts for dynamic args_main values before the final submit, prints reusable --set flags, and supports < for the previous item plus /skip for the current section.

When resolving tools from --toolProductUuid, the CLI caches the /tool/menus?is_all=1 result locally for 12 hours per profile + toolProductUuid to avoid repeated full-menu fetches.

Development

npm install
npm run build
node ./bin/run.js --help

Publish

npm publish

Autocomplete

oclif supports shell completion through @oclif/plugin-autocomplete.

Refresh the checked-in completion files in this repo with:

XT_CACHE_DIR=$PWD/.xtz-cache node ./bin/run.js autocomplete --refresh-cache

Install shell completion locally with:

xt autocomplete zsh
xt autocomplete bash
xt autocomplete powershell