GALAXY LAB YAML SCHEMA

This document describes the structure and validation rules for a Galaxy Lab section.yml file.

A minimal example of the full schema is shown below, but a real example would have more tabs and content items. Typically there should be only one section per YAML file (e.g. section_1.yml, section_2.yml).

    id: section_1
    title: Example section
    tabs:
      - id: tools
        title: Tools
        heading_md: Common tools are listed here, or search for more in the full tool panel to the left.
        content:
          - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc"
            title_md: `FastQC` - sequence quality reports
            description_md: |
              Before using your sequencing data, it’s important to ensure that
              the data quality is sufficient for your analysis.
            inputs:
              - label: Sequencing data for analysis
                datatypes:
                  - fasta
                  - fastq
                  - bam
                  - sam
      - id: workflows
        title: Workflows
        heading_md: |
          A workflow is a series of Galaxy tools that have been linked together
          to perform a specific analysis. You can use and customize the example workflows
          below.
          <a href="https://galaxyproject.org/learn/advanced-workflow/">
            Learn more
          </a>.
        content:
          - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222"
            button_tip: Import to Galaxy AU
            title_md: Data QC
            view_link: https://workflowhub.eu/workflows/222
            view_tip: View in WorkflowHub
            description_md: |
              Report statistics from sequencing reads.

              **Tools**

              - `nanoplot`
              - `fastqc`
              - `multiqc`

The above YAML results in the following element being rendered:

The YAML data above can be broken down into the following components:

1. Section
2. Section Tab
3. Tab Subsection
4. Content Item
5. Input Item
6. Button Icons

The YAML schema expects items 1-5 to be lists, so these elements can be repeated to provide as many Tabs, Content Items etc. as you like.

Section

Description

A Galaxy Lab section - this is the root of the section.yml file.

Properties

• id (string, required)
  Unique identifier for the section.

• title (string, required)
  Title of the section.

• tabs (array of SectionTab, required)
  List of tabs to be displayed for this section.

• exclude_from (array of strings or null, optional)
  List of Galaxy domain names (e.g. usegalaxy.eu) that this section should be excluded from e.g. if a feature is not implemented or tools are not available. Defaults to an empty array.

Example

    id: section_1
    title: Example section
    tabs:
      - <SectionTab>
      - <SectionTab>

Section Tab

Description

A tab with a list of expandable items to be shown in the section.

Properties

• id (string, required)
  Unique identifier for the tab.

• title (string or null, optional)
  Title of the tab.

• content (array of Content Items, object, or null, optional)
  A list of content items to be displayed in this tab. This can be omitted to create a tab with arbitrary MD/HTML content using the heading_md property. Can be any of:

  • An array of Content Items.
  • An object of { 'subsections': array of TabSubsections. }
  • null.

• heading_md (string or null, optional)
  Markdown or HTML formatted string for the heading. The value can be any length, so can even be extended to create a block of MD/HTML content.

• exclude_from (array of strings or null, optional)
  List of Galaxy domain names (e.g. usegalaxy.eu) that this tab should be excluded from e.g. if a feature is not implemented or tools are not available. Defaults to an empty array.

Example

    id: section_1_tools
    title: Tools
    heading_md: |
      These tools will get you started with your analysis.
      More advanced tools are available in the
      [next section](#advancedSection).
    content:
      - <ContentItem>
      - <ContentItem>

    id: section_1_tools
    title: Tools with subsections
    heading_md: |
      These tools are listed in subsections for easier navigation.
    content:
      subsections:
        - <TabSubsection>
        - <TabSubsection>

Tab Subsection

Description

A content subsection, to be used for dividing content into subsections, each with a title. e.g. "Short-read", "Long-read", "Hybrid".

Properties

• id (string, required)
  Unique identifier for the subsection.

• title (string, required)
  Title of the subsection.

• content (array of ContentItem, required)
  Content of the subsection.

• exclude_from (array of strings or null, optional)
  List of Galaxy domain names (e.g. usegalaxy.eu) that this tab subsection should be excluded from e.g. if a feature is not implemented or tools are not available. Defaults to an empty array.

Example

    id: tools_short_read
    title: These tools are optimized for short-read analysis
    content:
      - <ContentItem>
      - <ContentItem>

An example of this can be found on the Genome Lab, where subsections are used to separate Nanopore, Illumina and PacBio tools:

Content Item

Description

A content item, which is typically a Galaxy tool, workflow or tutorial. In the UI, this will be rendered as an "accordion" item. If button/view links are not specified, no buttons will be displayed. For tools and workflows, inputs can be used to describe the essential inputs.

When inserting URLs for the Galaxy server (e.g. link to Galaxy tool), ensure that you make use of the {{ galaxy_base_url }} variable to ensure that the link is correctly generated for different Galaxy servers! See below for an example.

Properties

• title_md (string, required)
  Markdown or HTML formatted title.

• description_md (string, required)
  Markdown or HTML formatted description.

• button_link (string or null, optional)
  URL for the button link - this is typically used as a "run" button for tools or workflows, but can be customized by setting the other button_* properties.

• button_tip (string or null, optional)
  Tooltip text for the button - this will be shown when the user's mouse passes over the item.

• button_md (string or null, optional)
  Markdown or HTML formatted string to display inside the "button" button.

• button_icon (ButtonIcon or null, optional)
  Icon for the button - must be one of the accepted ButtonIcon strings.

• view_link (string or null, optional)
  URL for the "view" link - this is typically a link to view more information about the item e.g. a workflow in WorkFlowHub.

• view_tip (string or null, optional)
  Tooltip text for the view - this will be shown when the user's mouse passes over the item.

• view_md (string or null, optional)
  Markdown or HTML formatted string to display inside the "view" button.

• view_icon (ButtonIcon or null, optional)
  Icon for the "view" button - must be one of the accepted ButtonIcon strings.

• exclude_from (array of strings or null, optional)
  List of Galaxy domain names (e.g. usegalaxy.eu) that this item should be excluded from e.g. if a feature is not implemented or a tool is not available. Defaults to an empty array.

Example

    - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc"
      title_md: `FastQC` - sequence quality reports
      description_md: |
          Before using your sequencing data, it’s important to ensure that
          the data quality is sufficient for your analysis.
      inputs:
        - <ItemInput>
        - <ItemInput>

The above YAML is rendered as:

    - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222"
      button_tip: Import to Galaxy Australia
      title_md: Data QC on Galaxy AU
      view_link: https://workflowhub.eu/workflows/222
      view_tip: View in WorkflowHub
      description_md: |
          Report statistics from sequencing reads.

          **Tools**

          - `nanoplot`
          - `fastqc`
          - `multiqc`
      exclude_from:
        - usegalaxy.org
        - usegalaxy.eu

The above YAML is rendered as:

You can create a workflow import URL as shown above from either DockStore or Workflowhub by changing the TRS ID and TRS server. The TRS ID can be found at the end of the URL of the workflow page on DockStore or Workflowhub.

InputItem

Description

An input dataset, typically for a Galaxy tool or workflow. The list of inputs will be displayed as a table.

Properties

• datatypes (array of strings, optional)
  List of accepted Galaxy datatypes for this input dataset. e.g. ['fastqsanger', 'fasta'].

• label (string or null, optional)
  Short description for the input dataset e.g. "Raw reads".

Example

    label: Raw reads
    datatypes:
      - fasta
      - fastqsanger

ButtonIcon

Description

Accepted icons identifiers for buttons.