Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/cwltool/schemas/v1.1/index.md @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author | shellac |
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date | Mon, 01 Jun 2020 08:59:25 -0400 (2020-06-01) |
parents | 79f47841a781 |
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--- a/env/lib/python3.7/site-packages/cwltool/schemas/v1.1/index.md Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ -# Common Workflow Language Specifications, v1.1 - -The CWL specifications are divided up into several documents. - -The [User Guide](http://www.commonwl.org/user_guide/) provides a gentle -introduction to writing CWL command line tools and workflows. - -The [Command Line Tool Description Specification](CommandLineTool.html) -specifies the document schema and execution semantics for wrapping and -executing command line tools. - -The [Workflow Description Specification](Workflow.html) specifies the document -schema and execution semantics for composing workflows from components such as -command line tools and other workflows. - -The -[Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html) -specifies the preprocessing steps that must be applied when loading CWL -documents and the schema language used to write the above specifications. - -Also available are inheritance graphs (as SVG images) for the [Schema Salad object model](salad.svg) and the [CWL object model](cwl.svg). - -# Running the CWL conformance tests - -Install a CWL runner of your choice. The reference runner can be installed as -the default runner by doing: -``` -pip install cwlref-runner -``` - -Install the CWL test parser: -``` -pip install cwltest -``` -You may need to activate a virtualenv first, or do a local install by adding `--user` after `install` above. - -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 -``` -./run_test.sh -``` - -If the CWL runner isn't installed as `cwl-runner` then you can specify the name for the runner: -``` -./run_test.sh RUNNER=cwltool -``` - -You can also specify additional options that are specific for the particular CWL runner you are using. -For example, with CWL reference runner you can turn on parallel execution mode: -``` -./run_test.sh RUNNER=cwltool EXTRA=--parallel -``` - -This can be combined with launching more than one CWL conformance test at once with `-j`: -``` -./run_test.sh -j4 RUNNER=cwltool EXTRA=--parallel -``` - -You can list all the tests -``` -./run_test.sh -l -``` - -You can run a particular test -``` -./run_test.sh -n23 -``` - - -If you are running tests for an unreleased CWL version use the `--enable-dev` flag: -``` -./run_test.sh EXTRA=--enable-dev -``` - - -For details of options you can pass to the test script, do: -``` -./run_test.sh --help -``` - -The full test suite takes about 10 minutes to run