Building Galaxy Tools

The following links are for the same tutorial describing the basics of how to build Galaxy tools. The first variant is tailored to local development environments (e.g. if Planemo has been installed with brew or pip) and the second is for developers using a dedicated Planemo virtual appliance (available as OVA, Docker, Vagrant, etc.).

• ...using Planemo
  • The Basics
  • Simple Parameters
  • Conditional Parameters
  • Wrapping a Script
  • Macros
  • Creating Galaxy tools from python scripts using argparse
  • More Information
• ...using a Planemo Virtual Appliance
  • The Basics
  • Simple Parameters
  • Conditional Parameters
  • Publishing to the Tool Shed
    • Configuring a Tool Shed Account
    • Creating a Repository
    • Updating a Repository
    • Serving a Tool from Shed
    • Main Tool Shed
  • Wrapping a Script
  • Macros
  • More Information

Additional tutorials include

• Advanced Tool Development Topics
  • Test-Driven Development
    • An Example Tool - BWA
    • Improved Input Handling via Test-Driven Development
    • Adding More Parameters
  • Multiple Output Files
    • Static Multiple Outputs
    • Static Outputs Determinable from Inputs
    • Single HTML Output
    • Dynamic Numbers of Outputs
      • Collections
      • Individual Datasets
        • Examples
        • More information
        • Legacy information
  • Collections
    • Consuming Collections
      • Processing Pairs
      • Processing Lists (Reductions)
      • Processing Identifiers
      • More on data_collection parameters
    • Creating Collections
      • 1. Static Element Count
      • 2. Computable Element Count
      • 3. Dynamic Element Count
      • Nested Collections
    • Further Reading
  • Macros - Reusable Elements
    • Direct XML Macros
    • Imported Macros
    • Parameterizing XML Macros (with yield)
    • Parameterizing XML Macros (with tokens)
    • Macro Tokens
  • Tool Provided Metadata
  • Cluster Usage
    • Developing for Clusters - GALAXY_SLOTS, GALAXY_MEMORY_MB, and GALAXY_MEMORY_MB_PER_SLOT
    • Test Against Clusters - --job_config_file
  • Dependencies and Conda
    • Specifying and Using Tool Requirements
    • Finding Existing Conda Packages
    • Exercise - Leveraging Bioconda
    • Building New Conda Packages
    • Exercise - Build a Recipe
  • Dependencies and Containers
    • BioContainers
      • Finding BioContainers
      • Building BioContainers
      • Publishing BioContainers
    • Explicit Annotation
• How do I... (Reference FAQ)
  • ... deal with index/reference data?
  • ... cite tools without an obvious DOI?
  • ... declare a Docker container for my tool?
  • ... do extra validation of parameters?
  • ... check input type in command blocks?
  • ... handle arbitrary output data formats?
  • ... determine the user submitting a job?
  • ... test with multiple value inputs?
  • ... test dataset collections?
  • ... test discovered datasets?
  • ... test composite dataset contents?
  • ... test index (.loc) data?
  • ... test exit codes?
  • ... test failure states?
  • ... test output filters work?
  • ... test metadata?
  • ... test tools installed in an existing Galaxy instance?
  • ... test tools against a package or container in a bioconda pull request?
  • ... interactively debug tool tests?