GA4GHV20

List all tools

Changed on

This endpoint returns all tools available or a filtered subset using metadata query parameters.

get/ga4gh/trs/v2/tools

Request

  • Base URL
    /api (relative, and the document was published on a file host, not at the API’s origin)
  • URL
    /api/ga4gh/trs/v2/tools
  • Auth
    HTTP bearer

Query parameters

idstring

A unique identifier of the tool, scoped to this registry, for example 123456.

aliasstring

Support for this parameter is optional for tool registries that support aliases. If provided will only return entries with the given alias.

toolClass'CommandLineTool' | 'Workflow'

Filter tools by the name of the subclass (#/definitions/ToolClass)

descriptorType'CWL' | 'WDL' | 'NFL' | 'GALAXY' | 'SMK' | 'SERVICE' | 'JUPYTER'

Filter tools by the name of the descriptor type

tagsstring[]

Filter tools by registry specific tags

registrystring

The image registry that contains the image.

organizationstring

The organization in the registry that published the image.

namestring

The name of the image.

toolnamestring

The name of the tool.

descriptionstring

The description of the tool.

authorstring

The author of the tool (TODO a thought occurs, are we assuming that the author of the CWL and the image are the same?).

checkerboolean

Return only checker workflows.

includeVersionsboolean

Support for this parameter is optional for tool registries. If false, the versions array of each returned tool will be empty. Use /tools/{id}/versions to retrieve the versions of a tool. If not specified in the request, versions are included.

offsetstring

Start index of paging. Pagination results can be based on numbers or other values chosen by the registry implementor (for example, SHA values). If this exceeds the current result set return an empty set. If not specified in the request, this will start at the beginning of the results.

limitinteger

Amount of records to return in a given page.

Response

An array of Tools that match the filter.

aliasesstring[]

Support for this parameter is optional for tool registries that support aliases. A list of strings that can be used to identify this tool which could be straight up URLs. This can be used to expose alternative ids (such as GUIDs) for a tool for registries. Can be used to match tools across registries.

checker_urlstring

Optional url to the checker tool that will exit successfully if this tool produced the expected result given test data.

descriptionstring

The description of the tool.

has_checkerboolean

Whether this tool has a checker tool associated with it.

idstring required

A unique identifier of the tool, scoped to this registry.

meta_versionstring

The version of this tool in the registry. Iterates when fields like the description, author, etc. are updated.

namestring

The name of the tool.

organizationstring required

The organization that published the image.

urlstring required

The URL for this tool in this registry.

Example response

[
  {
    "id": "123456",
    "url": "http://agora.broadinstitute.org/tools/123456",
    "versions": [
      {
        "descriptor_type_version": {
          "CWL": [
            "v1.0.2"
          ],
          "NFL": [
            "DSL2"
          ],
          "WDL": [
            "1.0",
            "1.1"
          ]
        },
        "id": "v1",
        "images": [
          {
            "checksum": [
              {
                "checksum": "77af4d6b9913e693e8d0b4b294fa62ade6054e6b2f1ffb617ac955dd63fb0182",
                "type": "sha256"
              }
            ],
            "image_name": "[\"quay.io/seqware/seqware_full/1.1\",\"ubuntu:latest\"]",
            "registry_host": "[\"registry.hub.docker.com\"]"
          }
        ],
        "included_apps": [
          "https://bio.tools/tool/mytum.de/SNAP2/1",
          "https://bio.tools/bioexcel_seqqc"
        ],
        "url": "http://agora.broadinstitute.org/tools/123456/versions/1"
      }
    ]
  }
]

Changes

  • d8be9581784cRevision changes
    • info

      added the new optional query request parameter includeVersions

    • info

      added the new optional query request parameter tags

    • info

      added the optional property /// to the response with the status