galaxy-tool-util

import os from galaxy.tool_util.parser import get_tool_source from galaxy.tool_util.linters import lint_tool_xml # Create a dummy tool XML file for demonstration tool_xml_content = """ <tool id="test_tool" name="Test Tool" version="1.0.0"> <description>A simple test tool</description> <command>echo "Hello World"</command> <inputs> <param name="input_text" type="text" label="Input text"/> </inputs> <outputs> <data name="output_file" format="txt" label="Output Text File"/> </outputs> <tests> <test> <param name="input_text" value="test"/> <output name="output_file" ftype="txt" value="Hello World" compare="re"/> </test> </tests> </tool> """ tool_path = "dummy_tool.xml" with open(tool_path, "w") as f: f.write(tool_xml_content) # 1. Parse the tool XML try: tool_source = get_tool_source(tool_path) print(f"Successfully parsed tool: {tool_source.parse_id()} (version {tool_source.parse_version()})") # 2. Linter (basic validation) # The lint_tool_xml function typically requires a tool_shed_repository mock for full functionality # For a simple local file, we can run it with minimal context. # In a real Galaxy environment, this would be part of a larger object. print("Running linter...") lint_problems = [] # The linter expects an XML root element, not a path directly. # For this quickstart, we'll demonstrate using a basic parse. from xml.etree import ElementTree root = ElementTree.parse(tool_path).getroot() # lint_tool_xml needs a ToolSource object, not just the root. # For a basic lint, you often need the full Galaxy context or specific mocks. # This example focuses on parsing. print("Basic parsing complete. Full linting requires more context.") except Exception as e: print(f"An error occurred: {e}") finally: # Clean up the dummy file if os.path.exists(tool_path): os.remove(tool_path)