galaxy/test/api/embed_test_1_tool.gxtool.yml at 6db36b419299bde5c4db206c20f8a8bb8765a805 - galaxy - Gitea: Git with a cup of tea

opensource/galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 02:04:04 +08:00

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T

John Chilton f6623b6e23 [WIP] Dynamic Galaxy tools.

- Introduce models and a API for creating tools dynamically.
 - Use Galaxy's testing-only YAML based representation of tools to prototype this.
 - Extend Format 2 workflow definitions to allow embedding tools directly into workflows, either directly or using a CWL-style @import syntax.

Testing:

Test cases demonstrating tools can be imported (only by admins) and are runnable are included with this commit. More test cases regarding workflow use of dynamic tools and Format 2 workflow definition extensions are also included.

These tests can be run with the following commands:

```
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_nonadmin_users_cannot_create_tools
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_dynamic_tool_1
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_import_export_dynamic
./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_workflow_embed_tool
./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_workflow_import_tool
```

2019-03-19 14:06:47 -04:00

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 class: GalaxyTool
 command: echo 'hello world 2' > $output1
 outputs:
   output1:
     format: txt