Ena Portal Tools#

Configuration File: ena_portal_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

ENAPortal_count_records (Type: ENAPortalTool)#

Count the number of records matching a query in the European Nucleotide Archive (ENA). Supports c…

ENAPortal_count_records tool specification

Tool Information:

  • Name: ENAPortal_count_records

  • Type: ENAPortalTool

  • Description: Count the number of records matching a query in the European Nucleotide Archive (ENA). Supports counting studies, samples, reads, and other result types. Useful for estimating dataset sizes before downloading. Example: counting studies with ‘description=”transcriptomics”’ returns ~9,000+, showing the breadth of transcriptomics data in ENA.

Parameters:

  • query (string) (required) ENA search query. Examples: ‘description=”cancer”’, ‘tax_tree(9606)’, ‘description=”CRISPR” AND tax_tree(10090)’.

  • result_type ([‘string’, ‘null’]) (optional) Type of records to count. Options: ‘study’, ‘sample’, ‘read_run’, ‘analysis’, ‘assembly’. Default: ‘study’.

Example Usage:

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

ENAPortal_search_runs_fastq (Type: ENAPortalTool)#

Search the European Nucleotide Archive (ENA) for sequencing RUNS (read_run) by taxonomy and libra…

ENAPortal_search_runs_fastq tool specification

Tool Information:

  • Name: ENAPortal_search_runs_fastq

  • Type: ENAPortalTool

  • Description: Search the European Nucleotide Archive (ENA) for sequencing RUNS (read_run) by taxonomy and library strategy, returning ready-to-use FASTQ download URLs. Metadata reports the exact matching count and whether the response is complete. ENA does not support offset pagination, so use a larger limit or the official limit=0 full-retrieval mode when all matching records are required. No API key required.

Parameters:

  • query (string) (required) ENA read_run query. Examples: ‘tax_eq(1280)’ (S. aureus, exact), ‘tax_tree(590)’ (Salmonella incl. descendants), ‘tax_eq(1280) AND library_strategy=”WGS”’. Plain keywords are auto-wrapped as description=”…”.

  • limit ([‘integer’, ‘null’]) (optional) Maximum runs to return (default 10). Use 0 to request every matching run, as defined by the ENA Portal API. ENA’s normal interface defaults to at most 100,000 records and has no offset pagination.

  • fields ([‘string’, ‘null’]) (optional) Comma-separated ENA run fields. Default: ‘run_accession,fastq_ftp,submitted_ftp,sra_ftp,fastq_md5,fastq_bytes,library_strategy,instrument_platform,read_count,scientific_name’.

Example Usage:

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

ENAPortal_search_samples (Type: ENAPortalTool)#

Search the European Nucleotide Archive (ENA) for biological samples by taxonomy or text query. Re…

ENAPortal_search_samples tool specification

Tool Information:

  • Name: ENAPortal_search_samples

  • Type: ENAPortalTool

  • Description: Search the European Nucleotide Archive (ENA) for biological samples by taxonomy or text query. Returns sample accessions, descriptions, taxonomy, and publication dates. Metadata reports the exact matching count and whether the response is complete. ENA does not support offset pagination, so use a larger limit or the official limit=0 full-retrieval mode when all matching records are required.

Parameters:

  • query (string) (required) ENA search query. Examples: ‘tax_tree(562)’ (E. coli), ‘description=”liver”’, ‘tax_tree(9606) AND description=”tumor”’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum results to return (default 10). Use 0 to request every matching record, as defined by the ENA Portal API. ENA’s normal interface defaults to at most 100,000 records and has no offset pagination.

  • fields ([‘string’, ‘null’]) (optional) Comma-separated fields. Default: ‘sample_accession,sample_alias,description,tax_id,scientific_name,first_public’.

Example Usage:

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

ENAPortal_search_studies (Type: ENAPortalTool)#

Search the European Nucleotide Archive (ENA) for sequencing studies using text queries or taxonom…

ENAPortal_search_studies tool specification

Tool Information:

  • Name: ENAPortal_search_studies

  • Type: ENAPortalTool

  • Description: Search the European Nucleotide Archive (ENA) for sequencing studies using text queries or taxonomy filters. Returns study accessions, titles, submitting centers, and publication dates. Metadata reports the exact matching count and whether the response is complete. ENA does not support offset pagination, so use a larger limit or the official limit=0 full-retrieval mode when all matching records are required.

Parameters:

  • query (string) (required) ENA search query. IMPORTANT: Plain text keywords (e.g., ‘cancer’) will cause HTTP 400. Always wrap text keywords with description=”…”. Examples: ‘description=”cancer”’, ‘tax_tree(9606)’ (human), ‘description=”transcriptomics” AND tax_tree(10090)’ (mouse transcriptomics).

  • limit ([‘integer’, ‘null’]) (optional) Maximum results to return (default 10). Use 0 to request every matching record, as defined by the ENA Portal API. ENA’s normal interface defaults to at most 100,000 records and has no offset pagination.

  • fields ([‘string’, ‘null’]) (optional) Comma-separated fields to return. Default: ‘study_accession,study_title,center_name,first_public,description’. Other fields: ‘last_updated,tax_id,scientific_name’.

Example Usage:

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