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comparison env/lib/python3.7/site-packages/cwltool/schemas/v1.1/index.md @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
| author | shellac |
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| date | Thu, 14 May 2020 14:56:58 -0400 |
| parents | 26e78fe6e8c4 |
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| 1:75ca89e9b81c | 2:6af9afd405e9 |
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| 1 # Common Workflow Language Specifications, v1.1 | |
| 2 | |
| 3 The CWL specifications are divided up into several documents. | |
| 4 | |
| 5 The [User Guide](http://www.commonwl.org/user_guide/) provides a gentle | |
| 6 introduction to writing CWL command line tools and workflows. | |
| 7 | |
| 8 The [Command Line Tool Description Specification](CommandLineTool.html) | |
| 9 specifies the document schema and execution semantics for wrapping and | |
| 10 executing command line tools. | |
| 11 | |
| 12 The [Workflow Description Specification](Workflow.html) specifies the document | |
| 13 schema and execution semantics for composing workflows from components such as | |
| 14 command line tools and other workflows. | |
| 15 | |
| 16 The | |
| 17 [Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html) | |
| 18 specifies the preprocessing steps that must be applied when loading CWL | |
| 19 documents and the schema language used to write the above specifications. | |
| 20 | |
| 21 Also available are inheritance graphs (as SVG images) for the [Schema Salad object model](salad.svg) and the [CWL object model](cwl.svg). | |
| 22 | |
| 23 # Running the CWL conformance tests | |
| 24 | |
| 25 Install a CWL runner of your choice. The reference runner can be installed as | |
| 26 the default runner by doing: | |
| 27 ``` | |
| 28 pip install cwlref-runner | |
| 29 ``` | |
| 30 | |
| 31 Install the CWL test parser: | |
| 32 ``` | |
| 33 pip install cwltest | |
| 34 ``` | |
| 35 You may need to activate a virtualenv first, or do a local install by adding `--user` after `install` above. | |
| 36 | |
| 37 From within a copy of [this repository](https://github.com/common-workflow-language/cwl-v1.1) (e.g. cwl-v1.1) execute the main test script | |
| 38 ``` | |
| 39 ./run_test.sh | |
| 40 ``` | |
| 41 | |
| 42 If the CWL runner isn't installed as `cwl-runner` then you can specify the name for the runner: | |
| 43 ``` | |
| 44 ./run_test.sh RUNNER=cwltool | |
| 45 ``` | |
| 46 | |
| 47 You can also specify additional options that are specific for the particular CWL runner you are using. | |
| 48 For example, with CWL reference runner you can turn on parallel execution mode: | |
| 49 ``` | |
| 50 ./run_test.sh RUNNER=cwltool EXTRA=--parallel | |
| 51 ``` | |
| 52 | |
| 53 This can be combined with launching more than one CWL conformance test at once with `-j`: | |
| 54 ``` | |
| 55 ./run_test.sh -j4 RUNNER=cwltool EXTRA=--parallel | |
| 56 ``` | |
| 57 | |
| 58 You can list all the tests | |
| 59 ``` | |
| 60 ./run_test.sh -l | |
| 61 ``` | |
| 62 | |
| 63 You can run a particular test | |
| 64 ``` | |
| 65 ./run_test.sh -n23 | |
| 66 ``` | |
| 67 | |
| 68 | |
| 69 If you are running tests for an unreleased CWL version use the `--enable-dev` flag: | |
| 70 ``` | |
| 71 ./run_test.sh EXTRA=--enable-dev | |
| 72 ``` | |
| 73 | |
| 74 | |
| 75 For details of options you can pass to the test script, do: | |
| 76 ``` | |
| 77 ./run_test.sh --help | |
| 78 ``` | |
| 79 | |
| 80 The full test suite takes about 10 minutes to run |