galaxy-tool-export-cbioportal-timeline

Overview

galaxy-tool-export-cbioportal-timeline is a Python-based tool designed to convert PyClone data to cBioPortal timeline format. This tool can be used as a standalone script or integrated into the Galaxy platform.

Features

• Converts PyClone data to cBioPortal timeline format.
• Generates meta and data files for cBioPortal.
• Supports exporting data to cBioPortal via an API endpoint.

Requirements

• Python 3.x
• pandas
• requests
• python-dotenv

Installation

Install the required Python packages using pip:

pip install -r requirements.txt

Usage

Standalone Script

To run the script standalone, use the following command:

python export_cbioportal_timeline.py --env_dir_path <path_to_env_file> --input_data <input_data_file> --study_id <study_id> --case_id <case_id> --meta_file_output <meta_file_output> --data_file_output <data_file_output> --timepoints <timepoints>

• --env_dir_path: Path to the .env file containing environment variables.
• --input_data: Input data file from history.
• --study_id: Study ID.
• --case_id: Case ID.
• --meta_file_output: Output meta file path.
• --data_file_output: Output data file path.
• --timepoints: String of timepoints separated by commas.

Galaxy Tool

This tool can also be used within the Galaxy platform. The corresponding XML configuration is provided in the export_cbioportal_timeline.xml file.

XML Configuration

The XML configuration file export_cbioportal_timeline.xml defines the tool for Galaxy:

• Tool ID: export_cbioportal_timeline
• Name: Load PyClone-VI output to cBioPortal Timeline
• Version: 1.0.3
• Description: Converts PyClone data to cBioPortal timeline format.

Inputs

• input_data: Input data file from history (tabular format).
• study_id: Study ID (default: nsclc_tracerx_2017).
• case_id: Case ID (default: CRUK0009).
• timepoints: Annotate timepoints of experiments.

Outputs

• meta_file: Meta Timeline file.
• data_file: Data Timeline file.

Example

python export_cbioportal_timeline.py --env_dir_path .env --input_data input_data.tsv --study_id nsclc_tracerx_2017 --case_id CRUK0009 --meta_file_output meta_timeline.txt --data_file_output data_timeline.txt --timepoints "LN1,1,,R1,10,,R2,20,,R3,30,,R4,40,,R5,50,,R6,60,,R7,70,"