Gdc Tools

Configuration File: gdc_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

GDC_list_files (Type: GDCFilesTool)

List GDC files filtered by data_type and other fields. Use to identify downloadable artifacts (e….

GDC_list_files tool specification

Tool Information:

  • Name: GDC_list_files

  • Type: GDCFilesTool

  • Description: List GDC files filtered by data_type and other fields. Use to identify downloadable artifacts (e.g., expression quantification) for analysis pipelines.

Parameters:

  • data_type (string) (optional) Data type filter (e.g., ‘Gene Expression Quantification’).

  • size (integer) (optional) Number of results (1–100).

  • offset (integer) (optional) Offset for pagination (0-based).

Example Usage:

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

GDC_search_cases (Type: GDCCasesTool)

Search cancer cohort cases in NCI GDC by project and filters. Use to retrieve case-level metadata…

GDC_search_cases tool specification

Tool Information:

  • Name: GDC_search_cases

  • Type: GDCCasesTool

  • Description: Search cancer cohort cases in NCI GDC by project and filters. Use to retrieve case-level metadata for cohort construction and downstream file queries.

Parameters:

  • project_id (string) (optional) GDC project identifier (e.g., ‘TCGA-BRCA’).

  • size (integer) (optional) Number of results (1–100).

  • offset (integer) (optional) Offset for pagination (0-based).

Example Usage:

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