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 * A tool interface generator is maintained at [[http://cli-mate.lumc.nl|http://cli-mate.lumc.nl]].
 * If you need to run an arbitrary working script (Python, Perl, R or Bash currently supported), and optionally turn it into a proper Galaxy tool, the [[https://bitbucket.org/fubar/galaxytoolfactory|Tool Factory]] can be installed in a local Galaxy from the Main Tool Shed to instantly wrap arbitrary scripts. It will turn these into Tool Shed archives ready to upload to a new repository from where they can be automagically installed into any Galaxy. **Only runs for administrative users** - exposes insecure unrestricted scripting, so only install in private development clones please. Generated tools are as secure as any other Galaxy tools.
 * Tool conversion and generation efforts:
  
* A tool interface generator is maintained at [[http://cli-mate.lumc.nl|http://cli-mate.lumc.nl]].
   * [[https://github.com/erasche/gxargparse|gxargparse]] - a drop in replacement of Python's argparse to generate Galaxy tools by Eric Rasche.
   * A [[https://groups.google.com/forum/#!searchin/common-workflow-language/galaxy/common-workflow-language/xa7HeDfIhw4/oAfg2Dk7ZHMJ|discussion]] on converting common workflow language tool descriptions into Galaxy tools - with prototype by Peter Amstutz.
  
* If you need to run an arbitrary working script (Python, Perl, R or Bash currently supported), and optionally turn it into a proper Galaxy tool, the [[https://bitbucket.org/fubar/galaxytoolfactory|Tool Factory]] can be installed in a local Galaxy from the Main Tool Shed to instantly wrap arbitrary scripts. It will turn these into Tool Shed archives ready to upload to a new repository from where they can be automagically installed into any Galaxy. **Only runs for administrative users** - exposes insecure unrestricted scripting, so only install in private development clones please. Generated tools are as secure as any other Galaxy tools.

More Tool Development Resources

  • A somewhat complete description of tags used for in tool XML files.

  • A place to share your tools with the community: the Galaxy Tool Shed - more information on publishing tools to the ToolShed.

  • Planemo a CLI tool to assist tool developer - easily lint, test, and preview your tools. (Quick Start, Planemo on Github)

  • A tutorial on writing of functional tests

  • What to do if Galaxy incorrectly reports that your tool failed to execute

  • Discussions on consuming and producing collections of datasets in tools.

  • A discussion on outputing multiple individual datasets

  • Tool conversion and generation efforts:
    • A tool interface generator is maintained at http://cli-mate.lumc.nl.

    • gxargparse - a drop in replacement of Python's argparse to generate Galaxy tools by Eric Rasche.

    • A discussion on converting common workflow language tool descriptions into Galaxy tools - with prototype by Peter Amstutz.

    • If you need to run an arbitrary working script (Python, Perl, R or Bash currently supported), and optionally turn it into a proper Galaxy tool, the Tool Factory can be installed in a local Galaxy from the Main Tool Shed to instantly wrap arbitrary scripts. It will turn these into Tool Shed archives ready to upload to a new repository from where they can be automagically installed into any Galaxy. **Only runs for administrative users** - exposes insecure unrestricted scripting, so only install in private development clones please. Generated tools are as secure as any other Galaxy tools.

  • Popular tool repositories on github to contribute to and serve as best practice examples: