Tools and resources table

One of the key features of the theme is support for a central tool and resource table. Tools that are mentioned in multiple places can be described once and reused across the website. These metadata fields can automatically populate a tools and resources table at the bottom of a page when the correct tool snippet is used in the page content.

Way of working

The all tools and resources list is based on the YAML file in the _data directory. Tools and resources can be manually linked to FAIRsharing.org, Bio.tools, TeSS and Europe PMC.

Prerequisites

• The main YAML file describing the tools is tool_and_resource_list.yml in /_data and must use valid YAML syntax.
• Make sure Markdown pages where you mention tools have a page_id in their front matter. The page_id should not contain hyphens; see the metadata documentation.
• When using the tool tag:
  • gem "elixir-toolkit-theme-plugins" is added to the /Gemfile
  • - elixir-toolkit-theme-plugins is added to the plugins block in the _config.yml file
  • A recent version of the ELIXIR Toolkit Theme is used. See the remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@VERSION line in the _config.yml file.
  • GitHub Actions is used to deploy the website. See instructions.

The main YAML file

Each tool or resource mentioned in the text has metadata stored in the main YAML file. The metadata block for each tool can contain the following attributes:

• id: The ID of a tool, in kebab-case, lowercase with hyphens.
• name: Name of the tool or resource.
• url: Main URL of the tool or resource. Make sure it starts with https://.
• description: Short description of the tool or resource. Avoid the characters " and '.
• registry: Four registries are supported: Bio.tools, FAIRsharing.org, TeSS and Europe PMC. Use the keys biotools, fairsharing, tess and europmc, specifying the ID or query after a colon. FAIRsharing records should use the DOI suffix, without the FAIRsharing. prefix. List registries under the registry attribute as key-value pairs.
• related_pages: List of page_id values. Avoid using this together with the {% tool "tool_id" %} snippet in the page text.
• how_to_access: Free-text field describing how the tool or resource can be accessed.

Example:

- id: github
  name: GitHub
  url: https://github.com
  description:
    Versioning system, used for sharing code, as well as for sharing of
    small data
  registry:
    tess: GitHub

NA as registry value is skipped and will not be rendered as a URL.

What tool or resource can be added to the table

Tools and resources specifically mentioned in page text should be present in the main table.

Adding new tools

1. Make sure the tool you want to add is not already described in the YAML file. If it is already present, go to step 3. If not, follow the next step.

2. Click the pencil icon in the GitHub view of the main YAML file, as described in our GitHub Guide. Add your tool or resource at the bottom of the file using the structure described in The main YAML file. Match the indentation of the existing items. When in doubt, validate the YAML before committing it.

3. Copy the tool_id of the tool or resource

4. Add the tool in the text using the following syntax:

    {% tool "tool_id" %}
   

   Examples:

   Use this snippet:

    {% tool "zenodo" %} is a powerful data publication service, which is supported by the European commission and focused on research data, including supplemental material like software, tables, figures or slides.
   

   This renders as:

   Zenodo is a powerful data publication service, which is supported by the European commission and focused on research data, including supplemental material like software, tables, figures or slides.

   Use this snippet:

    {% tool "beacon" %} is a GA4GH standard which enables standardised querying across multiple sources.
   

   This renders as:

   Beacon v2 with a very long name + description is a GA4GH standard which enables standardised querying across multiple sources.

Add double quotes around the tool_id and make sure to use the exact tool_id from the YAML file.

Listing all resources

By default, the table at the bottom of the page appears when tools are mentioned in the text or tagged with the correct page_id, as shown at the bottom of this page under “Tools and resources on this page”. To manually list all tools and resources described in your website, use this snippet:

{% include resource-table-all.html %}

This renders as:

Tools and resources on this page