ArticleBioinformatics (Oxford, England)2026
Coala: a standard-based framework for converting CWL-described command-line tools into agentic toolsets.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryLarge Language Models (LLM) can orchestrate computational analyses through agentic systems, but scaling their toolsets remains a barrier because tool definitions are often hard coded into agent implementation. We developed Command-line LLM-agent Adapter (Coala), a standard-based framework that bridges the Model Context Protocol (MCP) and the Common Workflow Language (CWL). Coala turns CWL tool descriptions into MCP-compatible, LLM-accessible schemas, treating tool definitions as data rather than code. Tools are then executed in containerized environments through a generic MCP server, which separates the agent's reasoning from tool execution. This framework improves reproducibility, reduces ongoing maintenance burden, and enables interactive access to local command-line tools through natural-language queries. AVAILABILITY AND IMPLEMENTATION: Coala is available at https://coala.info and is openly developed on GitHub: https://github.com/coala-info/coala.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.