galaxy-tool-plot-cluster-prevalence

Overview

galaxy-tool-plot-cluster-prevalence is a Python-based tool designed to plot the prevalence of clusters over samples from the TSV output of PyClone-VI. This tool can be integrated into the Galaxy platform using the provided XML configuration.

Features

• Reads TSV output from PyClone-VI.
• Plots cluster prevalence over samples using pandas, matplotlib, and seaborn.
• Generates area and line plots to visualize the data.
• Can be integrated into the Galaxy platform.

Requirements

• Python 3.x
• pandas (version 1.2.5)
• matplotlib (version 3.4.3)
• seaborn (version 0.11.2)

Installation

1. Clone the repository:

   git clone https://github.com/yourusername/galaxy-tool-plot-cluster-prevalence.git
   cd galaxy-tool-plot-cluster-prevalence

2. Install the required Python packages:

   pip install -r requirements.txt

Usage

To run the tool locally, use the following command:

python plot_clusters_prevalence.py --input_file path/to/your/input_file.tsv

Galaxy Integration

To integrate this tool into the Galaxy platform, use the provided plot_clusters_prevalence.xml file. This XML file defines the tool's configuration, including its requirements, inputs, outputs, and command to execute.

Steps to Integrate:

1. Place the plot_clusters_prevalence.xml file in the appropriate tools directory of your Galaxy instance.
2. Ensure the plot_clusters_prevalence.py script is accessible to the Galaxy tool configuration.
3. Restart your Galaxy instance to recognize the new tool.

Example

Here is an example command to run the tool:

python plot_clusters_prevalence.py --input_file example_data.tsv