Biotools Registry Tools

Configuration File: biotools_registry_tools.json Tool Type: Local Tools Count: 5

This page contains all tools defined in the biotools_registry_tools.json configuration file.

Available Tools

BioTools_get_tool (Type: BaseRESTTool)

Get detailed information about a specific bioinformatics tool from the ELIXIR Bio.tools registry …

BioTools_get_tool tool specification

Tool Information:

  • Name: BioTools_get_tool

  • Type: BaseRESTTool

  • Description: Get detailed information about a specific bioinformatics tool from the ELIXIR Bio.tools registry by its biotoolsID. Returns comprehensive metadata including name, description, homepage, tool type (command-line, web app, database, etc.), EDAM topics and operations, supported input/output data formats, programming languages, operating systems, license, documentation links, and credits. Use biotoolsID values discovered via BioTools_search. Example: ‘samtools’ for SAMtools, ‘blast’ for NCBI BLAST.

Parameters:

  • biotoolsID (string) (required) The unique Bio.tools identifier for the tool. Use lowercase. Examples: ‘samtools’, ‘blast’, ‘bwa’, ‘gatk’, ‘star’. Find IDs using BioTools_search.

  • format (string) (optional) Response format. Must be ‘json’.

Example Usage:

query = {
    "name": "BioTools_get_tool",
    "arguments": {
        "biotoolsID": "example_value"
    }
}
result = tu.run(query)

BioTools_search (Type: BaseRESTTool)

Search the ELIXIR Bio.tools registry for bioinformatics software tools, databases, and web servic…

BioTools_search tool specification

Tool Information:

  • Name: BioTools_search

  • Type: BaseRESTTool

  • Description: Search the ELIXIR Bio.tools registry for bioinformatics software tools, databases, and web services. Bio.tools is the comprehensive registry of bioinformatics resources maintained by ELIXIR, containing 30,000+ entries. Returns tool names, descriptions, types, topics, and homepages. Use this to find software for specific bioinformatics tasks (e.g., ‘sequence alignment’, ‘variant calling’, ‘protein structure prediction’). Example: search ‘RNA-seq’ to find RNA sequencing analysis tools.

Parameters:

  • q (string) (required) Free-text search query. Searches across tool names, descriptions, and topics. Examples: ‘blast’, ‘RNA-seq analysis’, ‘protein folding’, ‘variant calling’, ‘metagenomics’.

  • page (integer) (optional) Page number for paginated results (1-based). Default: 1.

  • size (integer) (optional) Number of results per page (1-50). Default: 10.

  • format (string) (optional) Response format. Must be ‘json’.

Example Usage:

query = {
    "name": "BioTools_search",
    "arguments": {
        "q": "example_value"
    }
}
result = tu.run(query)

BioTools_search_by_operation (Type: BaseRESTTool)

Search the ELIXIR Bio.tools registry for bioinformatics tools by EDAM operation (what the tool do…

BioTools_search_by_operation tool specification

Tool Information:

  • Name: BioTools_search_by_operation

  • Type: BaseRESTTool

  • Description: Search the ELIXIR Bio.tools registry for bioinformatics tools by EDAM operation (what the tool does). Returns tools that perform a specific computational operation. Useful operations include: ‘Sequence alignment’, ‘Structure prediction’, ‘Variant calling’, ‘Gene expression analysis’, ‘Phylogenetic inference’, ‘Protein function prediction’, ‘Molecular docking’, ‘Genome annotation’, ‘Visualisation’, ‘Data retrieval’, ‘Statistical calculation’, ‘Clustering’. Use this to find software for a specific analysis task.

Parameters:

  • operation (string) (required) EDAM operation name describing what the tool does. Examples: ‘Sequence alignment’, ‘Structure prediction’, ‘Variant calling’, ‘Molecular docking’, ‘Visualisation’, ‘Genome annotation’.

  • page (integer) (optional) Page number (1-based). Default: 1.

  • size (integer) (optional) Results per page (1-50). Default: 10.

  • format (string) (optional) Response format. Must be ‘json’.

Example Usage:

query = {
    "name": "BioTools_search_by_operation",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)

BioTools_search_by_topic (Type: BaseRESTTool)

Search the ELIXIR Bio.tools registry for bioinformatics tools by EDAM scientific topic. Returns t…

BioTools_search_by_topic tool specification

Tool Information:

  • Name: BioTools_search_by_topic

  • Type: BaseRESTTool

  • Description: Search the ELIXIR Bio.tools registry for bioinformatics tools by EDAM scientific topic. Returns tools classified under a specific research domain. Useful topics include: ‘Proteomics’, ‘Genomics’, ‘Transcriptomics’, ‘Structural biology’, ‘Phylogenetics’, ‘Metabolomics’, ‘Metagenomics’, ‘Epigenomics’, ‘Sequence analysis’, ‘Systems biology’, ‘Machine learning’, ‘Molecular interactions’, ‘Population genetics’. Use this to discover all available software for a specific research field.

Parameters:

  • topic (string) (required) EDAM topic name. Examples: ‘Proteomics’, ‘Genomics’, ‘Transcriptomics’, ‘Structural biology’, ‘Phylogenetics’, ‘Metabolomics’, ‘Metagenomics’, ‘Machine learning’, ‘Drug discovery’.

  • page (integer) (optional) Page number (1-based). Default: 1.

  • size (integer) (optional) Results per page (1-50). Default: 10.

  • format (string) (optional) Response format. Must be ‘json’.

Example Usage:

query = {
    "name": "BioTools_search_by_topic",
    "arguments": {
        "topic": "example_value"
    }
}
result = tu.run(query)

BioTools_search_by_type (Type: BaseRESTTool)

Search the ELIXIR Bio.tools registry for bioinformatics resources by tool type. Returns resources…

BioTools_search_by_type tool specification

Tool Information:

  • Name: BioTools_search_by_type

  • Type: BaseRESTTool

  • Description: Search the ELIXIR Bio.tools registry for bioinformatics resources by tool type. Returns resources of a specific category. Available types: ‘Command-line tool’, ‘Web application’, ‘Web API’, ‘Web service’, ‘Database portal’, ‘Desktop application’, ‘Library’, ‘Plug-in’, ‘Suite’, ‘Script’, ‘Workflow’, ‘Workbench’, ‘Ontology’, ‘Bioinformatics portal’. Use this to find, for example, all database portals or all web APIs for a research domain.

Parameters:

  • toolType (string) (required) Bio.tools resource type. Examples: ‘Command-line tool’, ‘Web application’, ‘Web API’, ‘Database portal’, ‘Library’, ‘Suite’, ‘Workflow’.

  • q ([‘string’, ‘null’]) (optional) Optional free-text query to further filter results. Example: ‘proteomics’ to find only proteomics-related tools of the specified type.

  • page (integer) (optional) Page number (1-based). Default: 1.

  • size (integer) (optional) Results per page (1-50). Default: 10.

  • format (string) (optional) Response format. Must be ‘json’.

Example Usage:

query = {
    "name": "BioTools_search_by_type",
    "arguments": {
        "toolType": "example_value"
    }
}
result = tu.run(query)