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Some improvements to Running Galaxy workflows
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- Renamed chapter "Interacting with Galaxy workflows"
  since it's covering a lot more than just planemo run.

- Introduced a few, new subheadings

- Hopefully improved explanation of workflow testing with planemo test
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wm75 committed Jan 31, 2024
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22 changes: 17 additions & 5 deletions docs/_running_intro.rst
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Expand Up @@ -28,6 +28,9 @@ the ``Number of lines`` parameter) are randomly selected. If you want to view
it in the Galaxy interface, you can do so with the command
``planemo workflow_edit tutorial.ga``.

Running a workflow
--------------------------------

The simplest way to run a workflow with planemo is on a locally hosted Galaxy
instance, just like executing a tool test with ``planemo test``. This can be
achieved with the command
Expand Down Expand Up @@ -71,7 +74,14 @@ of the user's choice. The full list of engines provided by Galaxy is:
``galaxy`` (the default, used in the first example above), ``docker_galaxy``,
``cwltool``, ``toil`` and ``external_galaxy``.

As a final example to demonstrate workflow testing, try:
Testing a workflow
--------------------------------

Testing a workflow can be thought of as an extension of running a workflow where,
after the run finishes, planemo asserts specified expectations about defined outputs.
Workflow tests, like tool tests, are performed with ``planemo test``.

As an example, try:

::

Expand Down Expand Up @@ -100,11 +110,13 @@ If you inspect its contents:
path: "data/output.txt"


you see that the job parameters are defined identically to the ``tutorial-job.yml``
file, with the addition of an output. For the test to pass, the output file
produced by the workflow must be identical to that stored in ``data/output.txt``.
you see that the ``job`` parameters, used to run the workflow, are defined identically to the
``tutorial-job.yml`` file, but that the test definition has an additional ``outputs`` section.
For the test to pass, the output file produced by the workflow must be identical to that stored in ``data/output.txt``.

More details about workflow testing can be found in the dedicated `Test Format <https://planemo.readthedocs.io/en/latest/test_format.html>`__ chapter.

The three commands above demonstrate the basics of workflow execution with
The examples above demonstrate the basics of workflow execution with
Planemo. For large scale workflow execution, however, it's likely that you would
prefer to use the more extensive resources provided by a public Galaxy server,
rather than running on a local instance. The tutorial therefore now turns to the
Expand Down
4 changes: 2 additions & 2 deletions docs/running.rst
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@@ -1,5 +1,5 @@
====================================
Running Galaxy workflows
Interacting with Galaxy workflows
====================================

Planemo offers a number of convenient commands for working with Galaxy
Expand All @@ -20,4 +20,4 @@ the ``planemo run`` command, which allows Galaxy tools and workflows to be
executed simply via the command line.

.. include:: _running_intro.rst
.. include:: _running_external.rst
.. include:: _running_external.rst

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