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gp-wrapper

Generate wrapper scripts for GenePattern modules with language selection and parameter handling.

1|4|Updated Sep 8, 2025
Search Tags:#script generation#bioinformatics#module development#wrapper script#GenePattern
One-click install
npx skills add https://github.com/genepattern/module-toolkit --skill gp-wrapper
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gp-wrapper
Source: https://github.com/genepattern/module-toolkit/tree/main/skills/gp-wrapper
Command: npx skills add https://github.com/genepattern/module-toolkit --skill gp-wrapper

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires genepattern, subprocess, argparse, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the creation of wrapper scripts for GenePattern modules, reducing the need for manual scripting and improving consistency.

Core Features & Use Cases

  • Automated Script Generation: Generates wrapper scripts for GenePattern modules based on tool specifications.
  • Language Selection: Automatically selects the appropriate scripting language based on the tool type.
  • Parameter Handling: Handles parameter requirements, including single/multi-value parameters and companion files.
  • Use Case: For a Python tool, the Skill generates a Python wrapper script that calls the tool using subprocess.

Quick Start

Generate a wrapper script for a Python tool by running: python generate_wrapper.py --tool-type python

Frequently Asked Questions about gp-wrapper

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate a GenePattern module wrapper script for a Python tool?▼

GenePattern wrapper scripts automate the integration of bioinformatics tools by handling parameter requirements and selecting the appropriate scripting language. This reduces manual scripting and improves consistency across modules.

Can I handle multi-value parameters and companion files when creating GenePattern modules?▼

Yes, automated GenePattern wrapper generation handles complex parameter requirements including single and multi-value parameters alongside companion files. This ensures all specified inputs are processed correctly within the module environment.

Do I need to provide tool specifications to automate GenePattern wrapper script generation?▼

Yes, you need to provide tool specifications and a GenePattern module environment. The wrapper generator uses these inputs to determine the appropriate scripting language and parameter handling for the bioinformatics tool.

Does GenePattern wrapper generation support scripting languages other than Python?▼

GenePattern wrapper script generation automatically selects the appropriate scripting language based on the provided tool type. While Python wrappers use subprocess for execution, the Skill adapts language selection to other specified bioinformatics tools.

Why use automated script generation for GenePattern bioinformatics modules instead of manual scripting?▼

Automated script generation for GenePattern modules reduces manual scripting effort and improves consistency. It standardizes how bioinformatics tools are wrapped, ensuring proper parameter handling and language selection across different integrations.

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