This extension provides XML validation, tags and attributes completion, help/documentation on hover, and other smart features to assist in following best practices recommended by the Intergalactic Utilities Commission during the development process of XML tool wrappers for Galaxy.
Please note this is still a work in progress so bugs and issues are expected. If you find any, you are welcome to open a new issue.
Requirements
Requires 
To use the Galaxy Language Server features you need Python 3.8+ installed on your system. See the Installation section for more details. The extension will create ins own Python virtual environment using python3-venv. You might need to install it in your system before installing the extension with apt install python3-venv.
Planemo
Since version 0.4.0 you can use some of the cool features of planemo directly from the extension. You only need to provide the required path to your planemo installation (see configuration) and the necessary parameters.
Table of Content
Installation
When the extension is activated for the first time, a notification will pop up informing that the Galaxy Language Server Python package must be installed.
The installation process will try to use the default Python version in your system. If the version is not compatible, it will ask you to enter the path to a compatible version. Just click Select in the notification message and you will be able to type the Python path at the top of the window.
This Python version is used to create a virtual environment in which the language server will be installed. Please note that on Debian/Ubuntu systems, you may need to install the python3-venv package to be able to create the virtual environment including pip, otherwise the installation may fail. Please see the Troubleshooting section below for more information.
Troubleshooting
If you encounter any problem during the language server installation, open the Visual Studio Code Console log and then find any error message with the [gls] prefix. You can access this log from the menu Help > Toggle Developer Tools > Console. Then, search the issues here to check whether the problem already has a solution. If not, please feel free to open a new issue including the error message from the console log.
Some possible errors:
The selected file is not a valid Python <version> path!. This message will appear if you select a Python binary that is not compatible with the required version. You will be given a chance to select the correct version the next time the extension gets activated. You can force it by reloading the extension or restarting VScode.
Error installing the Galaxy Language Server: pip module not found. The extension needs to create a virtual environment to install the galaxy-language-server package and its dependencies. To create a proper environment with pip included, in some systems you need to install the python3-venv package using the following command: apt install python3-venv (you might need to use sudo). Once you have python3-venv installed, try reloading VSCode and the extension should be installed successfully. If the extension installation keeps failing, you need to manually remove the glsenv directory inside the extension installation directory (usually ~/.vscode/extensions/davelopez.galaxy-tools-X.X.X/glsenv) and then restart or reload VSCode to recreate the environment.
Configuration
You can customize some of the features with various settings either placing them in the .vscode/settings.json file in your workspace or editing them through the Settings Editor UI.
Server settings
| Property |
Description |
galaxyTools.server.silentInstall |
Whether to skip user confirmation to install the language server. Useful when installing the extension in containers. |
Completion settings
| Property |
Description |
galaxyTools.completion.mode |
This setting controls the auto-completion of tags and attributes. You can choose between three different options: auto shows suggestions as you type; invoke shows suggestions only when you request them using the key shortcut (Ctrl + space); disabled completely disables the auto-completion feature. |
galaxyTools.completion.autoCloseTags |
This setting controls whether to auto-insert the closing tag after typing > or /. |
Planemo settings
Planemo integration is currently in experimental phase. Please report any problems you may encounter here.
| Property |
Description |
galaxyTools.planemo.enabled |
When enabled, you can use some of the planemo features directly from your editor. Please set #galaxyTools.planemo.envPath# to be able to use planemo. |
galaxyTools.planemo.envPath |
The full path to the Python virtual environment where planemo is installed. The path must end with planemo and be something like /<full-path-to-virtual-env>/bin/planemo. This is required to be able to use planemo features. |
galaxyTools.planemo.galaxyRoot |
The full path to the Galaxy root directory that will be used by planemo. This value will be passed to planemo as the parameter to --galaxy_root. This is required to be able to use some planemo features that need a running Galaxy instance. |
Testing Configuration
Planemo testing configuration
| Property |
Description |
galaxyTools.planemo.testing.enabled |
Whether to discover and run tests using planemo test directly from the Test Explorer. |
galaxyTools.planemo.testing.autoTestDiscoverOnSaveEnabled |
Whether to try to discover new tests when a Galaxy Tool Wrapper file is saved. |
galaxyTools.planemo.testing.extraParams |
Additional arguments that will be passed to planemo test command. |
Features
Tag and attribute auto-completion
The tags and attributes are suggested based on the Galaxy.xsd schema. They will appear in the same order that they are declared in the schema, so they can comply with the best practices recommendations defined in the Galaxy IUC Standards Style Guide.
Documentation on Hover
The documentation of tags and attributes is retrieved from the Galaxy.xsd schema.
Please note that some elements in the schema are still missing documentation. This will probably be improved over time.
Document validation
In addition to basic XML syntax validation, the tools are validated against the Galaxy.xsd schema.
Since version 0.8.0 the full Galaxy linting is directly reported on the document diagnostics.
When the tool file is saved it gets auto-formatted to comply with the Galaxy IUC Standards Style Guide.
Tag auto-closing
Whenever you write a closing (>), the corresponding closing tag will be inserted. You can also type / in an open tag to close it.
Snippets
Snippets can be really helpful to speed up your tool wrapper development. They allow you to quickly create common blocks and let you enter just the important information by pressing tab and navigating to the next available value.
If you want to add more snippets check the guide in the contribution guidelines.
Embedded syntax highlighting
Basic support for Cheetah and reStructuredText syntax highlighting inside the <command>, <configfile> and <help> tags. The embedded code should be inside a CDATA block.
Auto-generate tests
After you define the <inputs> and <outputs> of the tool, you can press Ctrl+Alt+t (or Cmd+Alt+t in Mac) to create a <tests> section with a basic structure and some test cases. This is especially useful when using conditionals and other nested parameters since you can get right away most of the boilerplate XML. You can always change the key bindings to your personal preference, see the documentation.
Auto-generate command section
Similar to the auto-generate tests command, but this time it will generate boilerplate Cheetah code for the <command> section.
Auto-sort param attributes
Now you can automatically sort the attributes of param elements according to the IUC Coding Style guidelines using a key-shortcut or the command palette. This can be done for each <param> element individually or for the full document.
Run planemo tests in the Test Explorer
You can now run planemo test for the currently opened tool directly from the Test Explorer.
- The tests are automatically discovered by the
galaxy-language-server when you open a tool or save the document (this can be controlled by the settings).
- You can then run all the tests from the
Test Explorer by using planemo test in the background. Currently running individual tests is not supported as AFAIK planemo does not have an option to do so at the moment.
- After successfully running the tests, the results will be displayed in a convenient way directly on your source XML.
The failing tests will be marked in red and the reason for failure can be seen directly beside the test definition (or you can right click the icon next to your test definition and choose Peek Error). You can also directly navigate to each of the tests XML source from the Test Explorer.
This can be very convenient especially when having a large number of tests in your tool.
Improved macros support
Since version 0.5.0 we added some interesting features around the use of macros. For example, you can now better troubleshoot validation errors caused by some included macro. The error messages will be more detailed and you can even navigate to a expanded version of the tool to see what the real tool document look like and what was causing the error.
There are also a lot of features around macros auto-completion. You can now navigate to macro and token definitions with F12 or get dynamic attribute auto-completion with parametrized macros and more.
You can select (a complete) XML element and then extract it to a local macro (directly in the tool wrapper) or into an external macro file. If there are several imported macro files, you can choose where to put them or if there is no imported file it will be created and imported directly.
Document Outline
You can now see a document outline of the currently opened tool document. This is especially useful when working with large tool documents. You can navigate to the different sections of the document in a quick and convenient way.
Insert Param Reference
Now you can use new commands to insert input parameter references into your wrapper. To insert a parameter reference in the command section, place your cursor in the desired position and then invoke the Insert a reference to a param element. command from the command palette (ctrl+shift+p) or directly use the default key binding for that command ctrl+alt+i ctrl+alt+p.
In a similar way, you can also invoke a command but for inserting a param reference that can be used inside an output filter. The default key binding for that is ctrl+alt+i ctrl+alt+f.
