Omics Tools

What it does

When your agent uses it

• The user asks to inspect h5ad files
• Summarize BAM regions
• Profile omics count tables
• Inventory mzML experiments before deeper modeling

Example prompts

• “Use the omics-tools skill to omic and single-cell workflow guide for AnnData, Scanpy-style dataset profiling, PyDESeq2-oriented count checks, pysam…”
• “/omics-tools”

Requirements

• Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

1. 1Start with structural profiling before statistical interpretation.
2. 2For single-cell data, inspect dimensions, metadata coverage, and top group counts before clustering or marker analysis.
3. 3For BAM or CRAM data, report mapped reads, index presence, and region counts before variant or expression conclusions.
4. 4For mzML data, summarize spectra and acquisition structure before quantification.
5. 5Save both a tabular output and a compact summary JSON.

What it can do on your machine

Read from SKILL.md and the folder at commit 960a6e0. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python3

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Omics Tools loads about 1.1k tokens when it runs. Until then it costs about 87 tokens; SKILL.md has 367 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~87

When it runs · the whole SKILL.md, loaded when a task matches

~1.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from DrugClaw/DrugClaw at commit 960a6e0, republished under its Apache-2.0 licence (© DrugClaw). 367 words, ~1,074 tokens.

name

omics-tools

description

Omics and single-cell workflow guide for AnnData, Scanpy-style dataset profiling, PyDESeq2-oriented count checks, pysam alignment inspection, and pyOpenMS mass-spectrometry summaries. Use when the user asks to inspect h5ad files, summarize BAM regions, profile omics count tables, or inventory mzML experiments before deeper modeling.

source

drugclaw

updated_at

2026-03-11

which python3 || true
python3 - <<'PY'
mods = ["pandas", "numpy", "anndata", "pysam"]
extra = ["scanpy", "pydeseq2", "pyopenms", "skbio"]
for name in mods + extra:
    try:
        __import__(name)
        print(f"{name}: ok")
    except Exception as exc:
        print(f"{name}: missing ({exc})")
PY

python3 templates/single_cell_profile.py \
  --input data/pbmc.h5ad \
  --cell-type-column cell_type \
  --group-column batch \
  --group-column donor \
  --output omics/pbmc_profile.csv \
  --summary omics/pbmc_profile.json

python3 templates/pysam_region_profile.py \
  --bam alignments/sample.bam \
  --region chr7:55019017-55211628 \
  --region chr12:25205246-25250928 \
  --output omics/sample_region_profile.csv \
  --summary omics/sample_region_profile.json

python3 templates/mzml_summary.py \
  --input proteomics/run01.mzML \
  --output omics/run01_mzml_profile.csv \
  --summary omics/run01_mzml_profile.json

© DrugClaw, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files in skills/science/omics-tools of DrugClaw/DrugClaw.

• SKILL.md
• templates/mzml_summary.py
• templates/pysam_region_profile.py
• templates/single_cell_profile.py

Open the folder on GitHubat commit 960a6e0