ToolDog

ToolDog generates Galaxy XML and Common Workflow Language (CWL) tool description templates by analyzing bioinformatics software source code and enriching those templates with metadata from the ELIXIR bio.tools registry to enable integration into Galaxy, Taverna, Chipster, and CWL-based workflows.

Key Features:

• Automated template generation: Generates Galaxy XML and CWL tool description templates from software source code and ELIXIR bio.tools registry metadata.
• Source Code Analysis Module: Uses language-specific plugins to analyze bioinformatics software source code and produce a skeleton Galaxy XML or CWL tool description.
• Metadata Enrichment Module: Enriches and corrects generated templates with metadata from the ELIXIR bio.tools registry, including parameters, publication links, and documentation references.
• Existing description updating: Updates or corrects existing tool descriptions to fill missing metadata fields.
• Targeted workflow systems: Produces descriptions intended for integration into Galaxy, Taverna, Chipster, and CWL-based workflow frameworks.

Scientific Applications:

• Workflow tool integration: Producing standardized tool descriptions to enable deployment of bioinformatics tools in Galaxy, Taverna, Chipster, and CWL workflows.
• Metadata curation: Automated extraction, enrichment, and correction of tool metadata using entries from the ELIXIR bio.tools registry.
• Reproducible workflow execution: Standardizing tool descriptions to support portable and reproducible execution of bioinformatics workflows.

Methodology:

ToolDog applies a dual-module approach: language-specific plugins analyze source code to generate an initial Galaxy XML or CWL skeleton, and a metadata enrichment module integrates metadata from the ELIXIR bio.tools registry to populate and correct the templates.