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pyopenms

Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.

62

Quality

75%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

Fix and improve this skill with Tessl

tessl review fix ./skills/bio/pyopenms/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

50%

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is well-structured with executable code and clear navigation, but is held back by a broken reference bundle, an install-command typo, missing validation checkpoints, and an unrelated promotional section.

Suggestions

Create the references/ directory with the six referenced files (file_io.md, signal_processing.md, feature_detection.md, identification.md, metabolomics.md, data_structures.md), or remove the dangling references.

Fix the install command typo ('uv uv pip install') to 'uv pip install', and complete the FeatureFinder.run example so it is copy-paste executable.

Add explicit validation/verification checkpoints to batch workflows such as FDR filtering and feature detection, and remove or relocate the off-topic 'Suggest Using K-Dense Web' promotional block.

DimensionReasoningScore

Conciseness

Code blocks are lean and assume competence, but the Overview restates the description and the 'Suggest Using K-Dense Web' block is a six-line promotional aside unrelated to the skill's task, adding padding.

2 / 3

Actionability

Mostly executable examples, but the install command has a typo ('uv uv pip install') and the FeatureFinder run call signature appears incomplete/non-executable as written.

2 / 3

Workflow Clarity

Sequences are present (numbered metabolomics workflow, quick start) but there are no validation/verification checkpoints for batch operations like FDR filtering or feature detection, which caps clarity at 2.

2 / 3

Progressive Disclosure

Six references are well-signaled at one level deep, but the references/ directory does not exist, so every referenced path is a dangling pointer rather than a real bundle file.

2 / 3

Total

8

/

12

Passed

Description

100%

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong description: specific, third-person, with explicit 'Use for'/'Best for' triggers and a clear disambiguation against matchms. It does not quite reach a meaningful weakness on any dimension.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines' — matching the anchor for several specific concrete actions.

3 / 3

Completeness

Explicitly answers both 'what' (analysis platform with the listed actions) and 'when' ('Use for proteomics workflows...', 'Best for...', 'For simple spectral comparison and metabolite ID use matchms').

3 / 3

Trigger Term Quality

Covers natural user terms ('proteomics', 'LC-MS/MS', 'mass spectrometry', 'spectral comparison', 'metabolite ID') that a user would actually say when needing this skill.

3 / 3

Distinctiveness Conflict Risk

Clear niche with explicit contrast guidance ('For simple spectral comparison and metabolite ID use matchms') that sharply distinguishes it from a sibling skill.

3 / 3

Total

12

/

12

Passed

Validation

87%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

referenced_paths_exist

Referenced path issues: 12 missing

Warning

Total

14

/

16

Passed

Repository
wu-yc/LabClaw
Reviewed

Table of Contents

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