Skill: billwanttobetop/auto-proteomics (version 0.2.1)

--- name: auto-proteomics description: Public OpenClaw skill for low-token routing and downstream analysis of processed DDA LFQ proteomics inputs. Use when the user already has protein-level quantification tables such as MaxQuant-style `proteinGroups.txt` and needs a clear two-group downstream workflow. --- # Auto Proteomics Author: Guo Xuan 郭轩 Contact: [REDACTED_SECRET] `auto-proteomics` is a public `v0.x` skill for processed proteomics downstream work. The current public promise is intentionally narrow: - one shipped runnable workflow: `dda-lfq-processed` - one public input family: processed DDA LFQ protein-level tables - one public comparison model: `group-a` vs `group-b` Everything else in this repository should be read as routing context, internal prototype, or future scaffold unless a document explicitly marks it as part of the public promise. Presence of a script, schema, or branch document does not mean the route is publicly supported. In particular, `dia-quant` is intentionally exposed as an internal prototype route for correct routing and contract validation, not as a shipped public workflow. ## Use this skill when - the user already has processed protein-level quantification output - the main table is MaxQuant-like `proteinGroups.txt` - the goal is QC, normalized matrix generation, and two-group differential protein analysis - the user wants a low-token, file-driven workflow instead of a long chat-only protocol ## Do not use this skill when - the user starts from raw spectra and needs search/identification - the request is primarily DIA, phosphoproteomics, enrichment, or multi-omics execution - the task requires more than one comparison design in the current release - the user only wants generic statistics with no proteomics context ## Public promise in `v0.x` Shipped and supported now: - route processed DDA LFQ downstream requests into `dda-lfq-processed` - validate the expected processed-input shape - generate matrix, QC, differential tables, report, and manifest outputs Not promised yet: - raw-spectrum search pipelines - DIA public execution support - phosphoproteomics execution - enrichment execution - multi-omics execution - generalized study-design handling beyond the current two-group path Internal prototype route available for routing only: - `dia-quant` may be selected only when the request is explicitly about processed DIA quant tables that fit the checked-in DIA contract - selecting `dia-quant` means internal prototype triage, never a public `v0.x` execution recommendation Important boundary: - non-shipped branches may contain scaffold or prototype execution files for internal framework development - smaller models must not treat those files as public runnable recommendations unless a route is explicitly marked `shipped` ## Minimal workflow 1. Read `references/WORKFLOW_INDEX.yaml` 2. If the route is unclear, run `scripts/decision/route_proteomics.py` 3. Check that the request fits the public `v0.x` boundary 4. Run `scripts/workflows/dda_lfq_processed.sh` 5. Use `references/` for runtime, onboarding, and development rules ## Public runnable entrypoint ```bash bash scripts/workflows/dda_lfq_processed.sh \ --input-dir <run_dir> \ --protein-groups <proteinGroups.txt> \ --summary <summary.txt> \ --parameters <parameters.txt> \ --output-dir <output_dir> \ --group-a <condition_a> \ --group-b <condition_b> ``` ## Input contract Required: - `proteinGroups.txt` with `LFQ intensity *` or `Intensity *` columns - `summary.txt` with `Raw file` and `Experiment` columns Optional: - `parameters.txt` ## Output contract The shipped workflow produces: - normalized protein matrix files under `matrix/` - QC outputs under `qc/` - differential protein tables under `stats/` - `REPORT.md` - `summary.json` - `run_manifest.json` ## Repository layers - `SKILL.md`: public entry and release boundary - `references/WORKFLOW_INDEX.yaml`: machine-readable routing and shipped-vs-non-shipped map - `references/BRANCH_FRAMEWORK.md`: standard branch contract for future routes - `references/branches/`: per-branch specs for scaffold and prototype workflows - `references/DIA_INPUT_SCHEMA.md`: first narrow schema for DIA prototype intake - `scripts/workflows/dda_lfq_processed.sh`: shipped workflow entrypoint - shipped public guidance lives in documents that explicitly describe the processed DDA `v0.x` path - non-shipped reference docs exist for internal framework development and must not be surfaced as public support ## Read next - `references/WORKFLOW_INDEX.yaml` - `references/RUNTIME_REQUIREMENTS.md` - `references/BRANCH_FRAMEWORK.md` - `references/DEMO_INPUT_GUIDE.md` - `references/DEVELOPMENT_GUIDE.md`


Security scan verdicts — ClawScan: clean | static analysis: clean | VirusTotal: clean | SkillSpector: clean (LOW)