ToolShed Readiness Checklist

The process from writing a tool to getting it into a ToolShed can be long and arduous and confusing. This checklist should assist in making sure you have done everything required for a great, easy to use Galaxy Tool!

Before ToolShed

  • A GitHub repository should exist for your wrappers, either one you own, or perhaps you are contributing to the IUC’s repository.
  • A tool directory should exist for the specific set of tools or related functionality you are wrapping.
  • Check Bioconda for available packages required for the tool you are wrapping. If they do not exist, you may need to create them. The IUC will be happy to help you with doing this.
  • Planemo should be installed (pip install -U planemo)
  • You will need to have credentials to access your ToolShed (either the Main ToolShed, or your local Galactic ToolShed).

Creating the Tool Wrapper (XML File)

  • Review the IUC’s Best Practices for Tools.
  • Consult the Galaxy Tool XML File schema.
  • Create your tool wrapper with a command like planemo tool_init --id 'tool_name' --name 'Tool description'.
  • Alternatively, you could copy and modify an existing IUC wrapper.
  • Give your tool an appropriate ID and name by consulting the IUC’s Best Practices for Tools. The ID is usually the same as the name of the tool XML file and directory.
  • Define a Tool Version for the wrapper. If it is the first wrapper, is recommended to use the same version as the tool in the requirement.
  • Add a short tool Description.
  • Fill in the Requirements section with the conda package name and version number for the tool and its dependencies.
  • Add the Version Command that specifies the command to get the tool’s version.
  • Add the Command section. The command to run the tool must be within CDATA tags, written in Cheetah and conform to PEP 8. You should add Exit Code detection and use single quotes for all Input and Output parameters of type data, data_collection and text.
  • Supply at least one Input with a description of parameters. Add Validators to user input fields.
  • Supply at least one Output with a description of parameters. For Output that is optionally created, use Filters.
  • Supply at least one Test. The primary output is a good choice for testing. Don’t forget the use of sim_size if variable data is included.
  • Add a Help section written in valid reStructuredText within CDATA tags.
  • Add a Citation section with a citation for the tool, preferably a DOI.
  • If your tool uses built-in data:
    • Provide the comment-only tool-data/data_table_name.loc.sample file
    • Provide the comment-only tool_data_table_conf.xml.sample file
  • Check that the XML elements and parameters attributes are in the Order specified in the Best Practices.
  • If you have a collection of related tools you can try to avoid duplicating XML by using a Macros XML file
  • Use 4 spaces for indentation.

Testing Your Tool

  • Fill the test-data directory with at least one input file and the expected output file.
  • It is strongly encouraged that you use small test data sets, ideally under 1 Mb. Every Galaxy instance that downloads your tool will have to download an entire copy of the test data. If the sum of your test-data files is larger than that, consider use of contains and test for a small subset of the output, see the CWPair2 example.
  • If your tool uses tool-data:
    • Provide a tool_data_table_conf.xml.test file, which is an uncommented version of tool_data_table_conf.xml.sample containing the path to the loc file for testing: <file path="${__HERE__}/test-data/data_table_name.loc" /> (Please note the use of ${__HERE__} to indicate the directory where the tool is).
    • Provide the .loc file: test-data/data_table_name.loc
    • For a good example of how to test parameters from data tables, please see the Bowtie example.
  • Check your tool XML with planemo lint.
  • Run functional tool tests in a local Galaxy with planemo test.
  • Serve the tool on a local Galaxy instance for manual verification that everything looks as expected with the planemo serve command.

Uploading Your Tool to a ToolShed

  • Ensure you have a .shed.yml file with the appropriate contents.
  • Check the .shed.yml with planemo shed_lint.
  • Create the remote repository with planemo shed_create --shed_target [toolshed|your_local_shed:9000].

Adding Your Tool to the IUC Repository

  • Create an issue on IUC GitHub, tracking your progress and ensuring that no one else is working on the same tool.
  • Fork IUC GitHub on your GitHub account.
  • Clone the corresponding repository git clone https://github.com/<YOUR_NAME>/tools-iuc tools-iuc
  • Within that folder, create a corresponding branch with git checkout -b $branch_name. You might name it after the tool.
  • After you have tested your tool and are completely happy with it (per previous sections of this document), add your tool and all associated data, then Commit the changes with git commit -m "I changed X, Y, and Z". Finally push your changes to github with git push origin $branch_name.
  • Go to the IUC’s Repository and click on ‘Compare & Pull Request’.
  • Add a comment describing what the tool and any extra information that might be needed (E.g. “I had some trouble with the data tables, can someone please double check them”).
  • The IUC will review your tool for inclusion.
  • Note that any Python code submitted to IUC must conform to PEP 8, in order to pass the flake8 Travis CI testing.