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Shanghua
96 lines
2.5 KiB
ReStructuredText
96 lines
2.5 KiB
ReStructuredText
Encode Tools
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============
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**Configuration File**: ``encode_tools.json``
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**Tool Type**: Local
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**Tools Count**: 2
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This page contains all tools defined in the ``encode_tools.json`` configuration file.
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Available Tools
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---------------
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**ENCODE_list_files** (Type: ENCODEFilesTool)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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List ENCODE files with filters (file_format, output_type, assay). Use to programmatically retriev...
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.. dropdown:: ENCODE_list_files tool specification
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**Tool Information:**
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* **Name**: ``ENCODE_list_files``
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* **Type**: ``ENCODEFilesTool``
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* **Description**: List ENCODE files with filters (file_format, output_type, assay). Use to programmatically retrieve downloadable artifact metadata (FASTQ, BAM, bigWig, peaks).
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**Parameters:**
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* ``file_type`` (string) (optional)
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File type filter (e.g., 'fastq', 'bam', 'bigWig').
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* ``assay_title`` (string) (optional)
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Assay filter (e.g., 'ChIP-seq').
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* ``limit`` (integer) (optional)
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Max number of results (1–100).
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**Example Usage:**
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.. code-block:: python
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query = {
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"name": "ENCODE_list_files",
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"arguments": {
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}
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}
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result = tu.run(query)
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**ENCODE_search_experiments** (Type: ENCODESearchTool)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Search ENCODE functional genomics experiments (e.g., ChIP-seq, ATAC-seq) by assay/target/organism...
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.. dropdown:: ENCODE_search_experiments tool specification
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**Tool Information:**
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* **Name**: ``ENCODE_search_experiments``
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* **Type**: ``ENCODESearchTool``
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* **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.
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**Parameters:**
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* ``assay_title`` (string) (optional)
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Assay name filter (e.g., 'ChIP-seq', 'ATAC-seq').
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* ``target`` (string) (optional)
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Target filter (e.g., 'CTCF').
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* ``organism`` (string) (optional)
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Organism filter (e.g., 'Homo sapiens', 'Mus musculus').
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* ``status`` (string) (optional)
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Record status filter (default 'released').
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* ``limit`` (integer) (optional)
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Max number of results (1–100).
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**Example Usage:**
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.. code-block:: python
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query = {
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"name": "ENCODE_search_experiments",
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"arguments": {
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}
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}
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result = tu.run(query)
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Navigation
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----------
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* :doc:`tools_config_index` - Back to Tools Overview
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* :doc:`../guide/loading_tools` - Loading Local Tools
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