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for Xiantao bioinformatics tools","maintainers":[{"name":"helixlife-ai","email":"helixlife.ai@gmail.com"}],"readme":"# xt\n\nCLI for Xiantao bioinformatics tools.\n\nInstall with `npm i -g @helixlife-ai/xiantao` and run it as `xt`.\n\n`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.\n\n`--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/helixlife/config.json`, and finally defaults to `opencode`. `--agent` is kept as a compatibility alias.\n\n`login`, `status`, and `logout` are the primary auth entrypoints. `exchange` redeems membership codes for the current profile. `auth ...` is kept as a compatibility topic and prints a migration warning when executed.\n\n## Main Flows\n\n### First Use\n\n```bash\nxt login\nxt tool search violin\nxt tool inspect violin_flat\nxt tool run violin_flat ./data.xlsx\n```\n\n`xt login` is the recommended first-use entrypoint. It authorizes and stores the profile token in one step. `xt tool login` is kept as an equivalent entrypoint under the `tool` topic.\n\n### Membership Exchange\n\n```bash\nxt exchange YOUR_CODE\nxt exchange YOUR_CODE --profile opencode --json\n```\n\n`xt exchange <code>` calls `/agent/ticket/exchange` with the current profile token and sends the exchange code as `code`. If an upstream API returns a membership-required 403 such as:\n\n```json\n{\n  \"success\": false,\n  \"code\": 403000101,\n  \"message\": \"您的账号暂无使用权限，需要购买会员，购买链接: https://www.helixlife.cn/main/vip\",\n  \"data\": {\n    \"vip_buy_link\": \"https://www.helixlife.cn/main/vip\"\n  }\n}\n```\n\nthe CLI reports both paths: open the returned purchase link to buy membership, or run `xt exchange <兑换码>` to redeem membership in the CLI.\n\n### Interactive Tool Run\n\n```bash\nxt tool run --interactive\n```\n\nThis 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.\n\n### Agent Automation\n\n```bash\nxt tool prepare violin_flat --file ./data.xlsx --profile opencode --json\nxt tool exec violin_flat --file ./data.xlsx --profile opencode --json\nxt tool exec violin_flat --file ./data.xlsx --profile opencode --json --download ./violin.pdf\n\nxt tool exec gsea_analysis --demo --profile opencode --json\nxt tool prepare gsea_plot --profile opencode --json\nxt tool exec gsea_plot --profile opencode --json --download ./gsea_plot.pdf\nxt tool exec gsea_customize --file gene_set=./gene_set.gmt --file data=./rank.xlsx --profile opencode --json\n\nxt tool cloud km_plot_gene --profile opencode --json --filter '胆管癌'\nxt tool exec km_plot_gene --profile opencode --json --cloudFilter '胆管癌'\nxt tool prepare km_plot_gene --profile opencode --json --cloudDataId tcga-chol-2\nxt tool exec km_plot_gene --profile opencode --json --cloudFilter '胆管癌' --cloudIndex 0\nxt tool exec km_plot_gene --profile opencode --json --cloudDataId tcga-chol-2\nxt tool specific-search km_plot_gene genes TP53 --profile opencode --json --cloudDataId tcga-brca-2\n```\n\nFor machine callers, use `xt tool prepare` to fetch the final schema, then `xt tool exec` to submit. Keep `--json`, pass an explicit profile with `--profile`, and avoid interactive-only flows.\nThe examples below illustrate command shapes, not a fixed allowlist of tools. Apply the same patterns to any tool with the same input mode.\n\n`xt tool prepare` and `xt tool exec` support the following input patterns:\n- upload modules: pass `--file <xlsx>`\n- multi-upload modules: repeat `--file key=path`, for example `--file gene_set=./gene_set.gmt --file data=./rank.xlsx`\n- demo-capable upload modules: pass `--demo`\n- history-record modules such as `gsea_plot`: pass neither `--file` nor `--demo`; the CLI reuses the default `XTRecord` returned by `tool inspect` / `tool prepare`\n- cloud-capable modules: use `xt tool cloud` to inspect candidates, then pass `--cloudFilter <keyword>`, `--cloudIndex <n>`, or `--cloudDataId <id>` to `tool prepare` / `tool exec`\n- modules without returned input metadata can be submitted with `--specific` / `--set`; the CLI sends an empty `args_data.info` payload\n\n`args_specific` defaults come from the dynamic schema returned by Xiantao. Use repeated `--specific` flags to override a whole key or a nested dotted path; array paths use numeric indexes.\n\n```bash\nxt tool prepare km_plot_gene --profile opencode --json --cloudDataId tcga-brca-2 --specific 'genes=TP53[ENSG00000141510.17]'\nxt tool prepare group_plot_clin --profile opencode --json --cloudDataId tcga-brca-2 --specific 'genes=[\"TP53[ENSG00000141510.17]\"]' --specific 'clin_list_1n.0.variable=(临床)Age'\nxt tool prepare cox_analysis_cloud --profile opencode --json --cloudDataId tcga-brca-2 --specific 'surv_list_nn.0.variable=(临床)Gender' --specific 'surv_list_nn.0.attrs_list.0.attrs=[\"Female [50]\",\"Male [49]\"]'\n```\n\nFor Search-style `args_specific` fields, use `xt tool specific-search <tool> <argsKey> <query> --json` to retrieve normalized choices before setting the final value. Pass the same input selectors that the tool needs, such as `--cloudDataId`, `--cloudFilter`, `--cloudIndex`, or `--selected`.\n\n### Cloud Data Flow\n\n`xt tool cloud` is the read-only helper for `XTCloud` modules. It lists candidate cloud records and only supports `--json`. Actual preparation and submission still happen through `xt tool prepare` and `xt tool exec`.\n\n```bash\nxt tool inspect km_plot_gene --profile opencode --json\nxt tool cloud km_plot_gene --profile opencode --json --filter '胆管癌'\nxt tool prepare km_plot_gene --profile opencode --json --cloudDataId tcga-chol-2\nxt tool exec km_plot_gene --profile opencode --json --cloudDataId tcga-chol-2\n```\n\nTypical cloud flow:\n- run `xt tool inspect <tool_id> --json` first and confirm `inputs.cloud_available=true`\n- run `xt tool cloud <tool_id> --json [--filter <keyword>]` to list candidates; use `data.choices[*].index` or `data_id` from the JSON output\n- if the filter matches one record, `tool prepare` / `tool exec` can use `--cloudFilter <keyword>` directly\n- if multiple records match, retry with `--cloudIndex <n>` or `--cloudDataId <id>`; `--cloudIndex` is 0-based\n- if you already have the full record payload, pass `--cloudRecordJson` or `--cloudRecordFile` to `tool prepare` / `tool exec`\n\nUseful cloud flags:\n- `xt tool cloud`: `--filter`, `--page`, `--all`, `--argsKey`, `--recordJson`, `--recordFile`\n- `xt tool prepare` / `xt tool exec`: `--cloudFilter`, `--cloudIndex`, `--cloudDataId`, `--cloudKey`, `--cloudRecordJson`, `--cloudRecordFile`\n\nCurrent operational notes for agent-style callers:\n- serialize `xt tool exec` submits per profile; Xiantao may reject overlapping or too-frequent submits with `NETWORK_ERROR`\n- `tool inspect` now includes the full `args_data` payload in JSON output and summarizes every detected `XTUpload` field\n- `tool inspect` also reports `inputs.cloud_available` and `inputs.cloud_default` for `XTCloud` modules\n- for multi-upload modules, pass keyed uploads in the same field names returned by `tool inspect`\n- `tool cloud` only supports `--json` and returns structured cloud candidates via `data.choices`\n- `tool specific-search` only supports `--json` and returns normalized dynamic `args_specific` choices via `data.choices`\n- if `tool prepare` or `tool exec` returns `code=TOOL_AMBIGUOUS` with `data.selection_type=cloud_record`, do not auto-pick; ask the user which item to use, then retry with `--cloudIndex` or `--cloudDataId`\n- if a command returns `code=PERMISSION_REQUIRED`, use the returned purchase link or redeem a membership code with `xt exchange <code> --profile <profile> --json`; do not treat it as a local input-file problem\n- if a command returns `code=RATE_LIMITED`, treat it as an upstream submit-capacity problem rather than changing local input files\n- `gsea_customize` has been validated through `tool prepare` and `tool exec` with repeated `--file gene_set=... --file data=...`\n\nFor agent workflows, do not use `xt tool run`. Treat `xt tool run` as the human-first path and `xt tool exec` as the machine path.\n\n`xt login --json` now returns the authorization link immediately and defaults to `authorized: false` until the browser step completes. Use `xt login --json --wait` when you explicitly want the command to block until authorization is confirmed. `xt status` is a probe-style check and returns `authorized: true` or `authorized: false` together with a reason such as `missing_token` or `expired_token`.\n\n## Command Groups\n\n### Auth\n\n- `xt login`\n- `xt status`\n- `xt logout`\n- `xt exchange`\n- `xt auth exchange`\n- `xt tool login`\n\n### Config\n\n- `xt config get agent_api`\n- `xt config set agent_api https://agent.helixlife.cn`\n- `xt config get base-url`\n- `xt config set base-url https://agent.helixlife.cn`\n- `xt config get login-url`\n- `xt config set login-url https://agent.helixlife.cn/`\n\n### History\n\n- `xt history list`\n- `xt history view`\n- `xt history download`\n- `xt history save`\n- `xt history rename`\n- `xt history delete`\n\n### Tool Run\n\n- `xt tool search`\n- `xt tool inspect`\n- `xt tool cloud`\n- `xt tool specific-search`\n- `xt tool prepare`\n- `xt tool run`\n- `xt tool exec`\n- `xt tool download`\n\n### Tool Debug\n\n- `xt tool resolve`\n- `xt tool menu`\n- `xt tool menus`\n- `xt tool menus-raw`\n- `xt tool fetch-all`\n\n## Notes\n\nFor Xiantao tool commands that accept `--toolProductUuid`, the default value is `c0b6febb-52dd-4525-970a-61bbe9e263ff`. You can override it with `--toolProductUuid`, `XIANTAO_TOOL_PRODUCT_UUID`, or `~/.config/helixlife/config.json` under `xiantao.toolProductUuid`.\n\nThe CLI also loads a project-root `.env` file on startup. You can set `XIANTAO_BASE_URL=https://agent.helixlife.cn` there to switch the API base URL without prefixing each command manually, and `XIANTAO_LOGIN_URL=https://agent.helixlife.cn/` to override the resolved login page value. The same values can be stored with `xt config set agent_api ...` and `xt config set login-url ...`; `base-url` is kept as a compatibility alias for `agent_api`. Environment variables take precedence over `~/.config/helixlife/config.json`. Login stores the access token at `~/.config/helixlife/user-access-token.txt`. `xt exchange <code>` uses that token to redeem membership through `/agent/ticket/exchange`. Set `DEBUG_MODE=1` to print HTTP request and response debug payloads to stderr.\n\n`xt tool search <keyword>` searches 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, the full `args_data` payload in JSON mode, and the detected input source summary, including `XTCloud`, per-field `XTUpload`, and `XTRecord` defaults. `xt tool specific-search <tool_id> <argsKey> <query> --json` searches dynamic Search-style `args_specific` options and strips frontend highlight markup from returned choices. `xt tool run <tool_id>` runs a Xiantao bioinformatics tool in the human-first path. `xt tool exec <tool_id>` is the agent-safe submit command and also supports `--download <path>` when a local artifact is needed. `xt tool resolve <tool_id>` remains available as the low-level UUID and route lookup. `xt tool menus` returns a concise catalog with each tool title, `module_id`, `path`, and `route`, which is useful when `tool search` finds nothing helpful or when you want to shortlist tools for recommendation.\n\n`xt tool cloud <tool_id>` fetches paginated cloud candidates and returns a machine-friendly payload when `--json` is used. `data.choices` contains the short selector list with 0-based `index`, `data_id`, and `label`; `records` contains the full records; `columns`, `filter`, `selected_record`, `pages_fetched`, and pagination metadata are included for callers that need the full context. Use `--page` to fetch one page, `--all` to merge every page, and `--argsKey` only when the module's cloud field cannot be auto-detected. `xt tool cloud` uses `--recordJson` / `--recordFile` for the current record seed, while `xt tool prepare` and `xt tool exec` use `--cloudRecordJson` / `--cloudRecordFile` for the final selected record.\n\n`--demo` reuses the demo file metadata returned by `tool fetch-all`; `--file` uploads a local file first; multi-upload modules accept repeated `--file key=path`; for `XTRecord` modules the CLI can submit directly from the default history record returned by `fetch-all`; for `XTCloud` modules use `--cloudFilter`, then `--cloudIndex` or `--cloudDataId` to pin one cloud record before submit. Tools that return no input metadata can still submit in `mode=none` with `--set` / `--specific`; the CLI sends an empty `args_data.info` object. Run `xt login` first to authorize the stored token. When cloud filtering matches multiple records, `tool prepare` and `tool exec` return `code=TOOL_AMBIGUOUS` plus `data.selection_type=cloud_record` and `data.choices`; callers should ask the user which record to use before retrying. `--cloudRecordJson` / `--cloudRecordFile` cannot be combined with `--cloudFilter` / `--cloudDataId` / `--cloudIndex`, and cloud selection flags cannot be combined with `--demo` or `--file`. When a tool exposes multiple downloadable results, `--download <path>` uses the output file extension to select the matching artifact.\n\nFor the current GSEA tool family, `gsea_plot`, `gsea_plot2`, `gsea_bar`, `gsea_point`, `gsea_ridge`, `gsea_emapplot`, `gsea_tree`, and `gsea_path_cluster` are record-backed visual modules that reuse the default `gsea_analysis` history record. `gsea_analysis` itself is an upload/demo analysis module. `gsea_customize` is a custom gene-set upload module whose frontend expects two uploads, `gene_set` and `data`; submit it with `--file gene_set=... --file data=...`. A real CLI submit path has been verified with the sample files in [`docs/GSEA-基因集.csv`](/Users/chenyunjie/Desktop/xtz-cli/xiantao/docs/GSEA-基因集.csv) and [`docs/GSEA-分子.xlsx`](/Users/chenyunjie/Desktop/xtz-cli/xiantao/docs/GSEA-分子.xlsx).\n\n`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.\n\n`xt history list` lists the current profile's history records and shows the latest `fuid`, status, module, and time for each record. `xt history view <fuid>` lists the downloadable files for one history record. `xt history download <fuid> --device pdf` downloads an existing history artifact by `fuid`; when a record exposes multiple files, pass `--device`, `--item`, `--label`, or use an `--output` path with a target extension. `xt history save <fuid> <uuid> <module_id> <name>` saves a direct analysis result into history. `xt history rename <fuid> <name>` renames a record, and `xt history delete <fuid>` deletes it.\n\n## Development\n\n```bash\nnpm install\nnpm run build\nnode ./bin/run.js --help\n```\n\n## Publish\n\n```bash\nnpm publish\n```\n\n## Autocomplete\n\noclif supports shell completion through `@oclif/plugin-autocomplete`.\n\nRefresh the checked-in completion files in this repo with:\n\n```bash\nXT_CACHE_DIR=$PWD/.xtz-cache node ./bin/run.js autocomplete --refresh-cache\n```\n\nInstall shell completion locally with:\n\n```bash\nxt autocomplete zsh\nxt autocomplete bash\nxt autocomplete powershell\n```\n","readmeFilename":"README.md"}