Encode Tools

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

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

Available Tools

ENCODE_list_files (Type: ENCODEFilesTool)

List ENCODE files with filters (file_format, output_type, assay). Use to programmatically retriev…

ENCODE_list_files tool specification

Tool Information:

  • Name: ENCODE_list_files

  • Type: ENCODEFilesTool

  • Description: List ENCODE files with filters (file_format, output_type, assay). Use to programmatically retrieve downloadable artifact metadata (FASTQ, BAM, bigWig, peaks).

Parameters:

  • file_type (string) (optional) File type filter (e.g., ‘fastq’, ‘bam’, ‘bigWig’).

  • assay_title (string) (optional) Assay filter (e.g., ‘ChIP-seq’).

  • limit (integer) (optional) Max number of results (1–100).

Example Usage:

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

ENCODE_search_experiments (Type: ENCODESearchTool)

Search ENCODE functional genomics experiments (e.g., ChIP-seq, ATAC-seq) by assay/target/organism…

ENCODE_search_experiments tool specification

Tool Information:

  • Name: ENCODE_search_experiments

  • Type: ENCODESearchTool

  • Description: Search ENCODE functional genomics experiments (e.g., ChIP-seq, ATAC-seq) by assay/target/organism/status. Use to discover datasets and access experiment-level metadata.

Parameters:

  • assay_title (string) (optional) Assay name filter (e.g., ‘ChIP-seq’, ‘ATAC-seq’).

  • target (string) (optional) Target filter (e.g., ‘CTCF’).

  • organism (string) (optional) Organism filter (e.g., ‘Homo sapiens’, ‘Mus musculus’).

  • status (string) (optional) Record status filter (default ‘released’).

  • limit (integer) (optional) Max number of results (1–100).

Example Usage:

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