Ega Tools#

Configuration File: ega_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

EGA_get_dataset (Type: EGATool)#

Resolve an EGA dataset accession to its public metadata: technology platform, sample count, and a…

EGA_get_dataset tool specification

Tool Information:

  • Name: EGA_get_dataset

  • Type: EGATool

  • Description: Resolve an EGA dataset accession to its public metadata: technology platform, sample count, and access policy. Example: accession=’EGAD00000000001’ returns an Affymetrix 500K genotyping dataset of 1,504 samples under controlled access. Metadata only – the underlying data requires Data Access Committee approval via the returned policy_accession_id.

Parameters:

  • accession (string) (required) EGA dataset accession, e.g. ‘EGAD00000000001’.

Example Usage:

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

EGA_get_study (Type: EGATool)#

Resolve an EGA (European Genome-phenome Archive) study accession to its public metadata: title, d…

EGA_get_study tool specification

Tool Information:

  • Name: EGA_get_study

  • Type: EGATool

  • Description: Resolve an EGA (European Genome-phenome Archive) study accession to its public metadata: title, description, study type, and publication. Example: accession=’EGAS00000000001’ returns the WTCCC bipolar disorder case-control study. Metadata only – the underlying controlled-access sequence/genotype data requires separate Data Access Committee approval. Use EGA_get_study_datasets to find the study’s dataset accessions.

Parameters:

  • accession (string) (required) EGA study accession, e.g. ‘EGAS00000000001’.

Example Usage:

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

EGA_get_study_datasets (Type: EGATool)#

List the dataset accessions belonging to one EGA study. Example: accession=’EGAS00000000001’ retu…

EGA_get_study_datasets tool specification

Tool Information:

  • Name: EGA_get_study_datasets

  • Type: EGATool

  • Description: List the dataset accessions belonging to one EGA study. Example: accession=’EGAS00000000001’ returns its constituent EGAD dataset(s) with technology and sample count. Use EGA_get_study to find a study accession first, then EGA_get_dataset for full details on any returned dataset.

Parameters:

  • accession (string) (required) EGA study accession, e.g. ‘EGAS00000000001’.

Example Usage:

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