Galaxy Workflow Format 2 Descriptions
Project description
galaxy-workflow-tool-tests
A simple wrapper around Galaxy’s galaxy-tool-test that runs tool tests for all the tools in a workflow.
Minimal Usage:
galaxy-workflow-tool-tests -k <api_key> -u http://localhost:8080/ <encoded_workflow_id>
Program Help
$ galaxy-workflow-tool-tests --help usage: galaxy-workflow-tool-tests [-h] [-u GALAXY_URL] [-k KEY] [-a ADMIN_KEY] [--force_path_paste] [-t TOOL_ID] [--tool-version TOOL_VERSION] [-i TEST_INDEX] [-o OUTPUT] [--append] [--skip-previously-executed | --skip-previously-successful] [-j OUTPUT_JSON] [--verbose] [-c CLIENT_TEST_CONFIG] [--suite-name SUITE_NAME] [--with-reference-data] [--skip-with-reference-data] [--history-per-suite | --history-per-test-case] [--no-history-cleanup] [--publish-history] [--parallel-tests PARALLEL_TESTS] [--retries RETRIES] [--page-size PAGE_SIZE] [--page-number PAGE_NUMBER] [--download-attempts DOWNLOAD_ATTEMPTS] [--download-sleep DOWNLOAD_SLEEP] [--test-data TEST_DATA] WORKFLOW_ID Script to quickly run a tool test against a running Galaxy instance. positional arguments: WORKFLOW_ID workflow id to scan for tools optional arguments: -h, --help show this help message and exit -u GALAXY_URL, --galaxy-url GALAXY_URL Galaxy URL -k KEY, --key KEY Galaxy User API Key -a ADMIN_KEY, --admin-key ADMIN_KEY Galaxy Admin API Key --force_path_paste This requires Galaxy-side config option "allow_path_paste" enabled. Allows for fetching test data locally. Only for admins. -t TOOL_ID, --tool-id TOOL_ID Tool ID --tool-version TOOL_VERSION Tool Version (if tool id supplied). Defaults to just latest version, use * to test all versions -i TEST_INDEX, --test-index TEST_INDEX Tool Test Index (starting at 0) - by default all tests will run. -o OUTPUT, --output OUTPUT directory to dump outputs to --append Extend a test record json (created with --output-json) with additional tests. --skip-previously-executed When used with --append, skip any test previously executed. --skip-previously-successful When used with --append, skip any test previously executed successfully. -j OUTPUT_JSON, --output-json OUTPUT_JSON output metadata json --verbose Verbose logging. -c CLIENT_TEST_CONFIG, --client-test-config CLIENT_TEST_CONFIG Test config YAML to help with client testing --suite-name SUITE_NAME Suite name for tool test output --with-reference-data --skip-with-reference-data Skip tests the Galaxy server believes use data tables or loc files. --history-per-suite Create new history per test suite (all tests in same history). --history-per-test-case Create new history per test case. --no-history-cleanup Perserve histories created for testing. --publish-history Publish test history. Useful for CI testing. --parallel-tests PARALLEL_TESTS Parallel tests. --retries RETRIES Retry failed tests. --page-size PAGE_SIZE If positive, use pagination and just run one 'page' to tool tests. --page-number PAGE_NUMBER If page size is used, run this 'page' of tests - starts with 0. --download-attempts DOWNLOAD_ATTEMPTS Galaxy may return a transient 500 status code for download if test results are written but not yet accessible. --download-sleep DOWNLOAD_SLEEP If download attempts is greater than 1, the amount to sleep between download attempts. --test-data TEST_DATA Add local test data path to search for missing test data
History
0.0.2 (2020-12-16)
Fixes to project structure for PyPI.
0.0.1 (2020-12-16)
Initial testing release.
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