.. image:: https://readthedocs.org/projects/gxformat2/badge/?version=latest
:target: https://gxformat2.readthedocs.io/en/latest/
.. image:: https://badge.fury.io/py/gxformat2.svg
:target: https://pypi.python.org/pypi/gxformat2/
.. image:: https://github.com/galaxyproject/gxformat2/workflows/Python%20CI/badge.svg
:target: https://github.com/galaxyproject/gxformat2/actions?query=workflow%3A%22Python+CI%22
.. image:: https://github.com/galaxyproject/gxformat2/workflows/Java%20CI/badge.svg
:target: https://github.com/galaxyproject/gxformat2/actions?query=workflow%3A%22Java+CI%22
.. image:: https://img.shields.io/badge/latest%20schema-v19.09-blue
:target: https://galaxyproject.github.io/gxformat2/v19_09.html
Format 2
--------
This package defines a high-level Galaxy_ workflow description termed "Format
2". The current schema version is v19_09 and the schema can be found
`here <https://galaxyproject.github.io/gxformat2/v19_09.html>`__. This version of
workflow format can be consumed by Galaxy since version 19.09.
The Format 2 workflow description is still somewhat experimental and may
yet change in small potentially backward incompatible ways until the format is
exported by Galaxy by default.
The traditional Galaxy workflow description (files ending in ``.ga`` extension,
sometimes called native workflows in this project) was not designed to be
concise and is neither readily human readable or human writable. Galaxy
workflow Format 2 is being designed to address these limitations,
while also moving Galaxy's workflow description language toward standards such
as the Common Workflow Language.
gxformat2
---------
This Python project can be installed from PyPI using ``pip``.
::
$ pip install gxformat2
Checkout the project tests or how it used in projects such as Planemo and
Galaxy to see how to use the gxformat2 library. Reference documentation for
the `modules <https://gxformat2.readthedocs.io/en/latest/py-modindex.html>`__
can be found as part of the project's documentation.
This project also includes various scripts for working with Galaxy workflows.
Checkout their help for more information.
::
$ gxwf-lint --help
$ gxwf-viz --help
$ gxwf-abstract-export --help
This library and associated scripts are licensed under the MIT License.
.. _Galaxy: https://galaxyproject.org/
History
-------
.. to_doc
---------------------
0.19.0 (2024-07-23)
---------------------
* Sync markdown_parse with Galaxy (thanks to `@mvdbeek`_). `Pull Request 99`_
* More helpers for reasoning about gxformat2 steps (thanks to `@jmchilton`_).
`Pull Request 98`_
* Add abstraction for popping connection dictionary to model (thanks to
`@jmchilton`_). `Pull Request 96`_
* Add now mandatory readthedocs config files (thanks to `@nsoranzo`_). `Pull
Request 94`_
* Use `ConnectedValue` for connected values (thanks to `@mvdbeek`_). `Pull
Request 95`_
* Refresh codegen using schema-salad 8.4.20230808163024 (thanks to `@mr-c`_).
`Pull Request 92`_
* Update label comment (thanks to `@mvdbeek`_). `Pull Request 90`_
---------------------
0.18.0 (2023-05-12)
---------------------
* Fix input conversion if input has no label by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/89
---------------------
0.17.0 (2023-01-06)
---------------------
* Enable "when" for workflow steps by @mr-c in https://github.com/galaxyproject/gxformat2/pull/74
* When fixes by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/86
---------------------
0.16.0 (2022-09-20)
---------------------
* Add dev ``when`` on steps to backend (don't expose in schema yet). by @jmchilton in https://github.com/galaxyproject/gxformat2/pull/48
* Update project plumbing to allow dev release. by @jmchilton in https://github.com/galaxyproject/gxformat2/pull/49
* Drop support for Python 3.5, add 3.9 by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/52
* Relicense under the MIT license by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/58
* Format2: Add `label` attribute to `WorkflowInputParameter` and `WorkflowOutputParameter` by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/56
* Misc fixes and refactorings by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/55
* Convert Format2 workflow `label` to native `name` by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/54
* test_abstract_export: use different names for the different outputs by @simleo in https://github.com/galaxyproject/gxformat2/pull/57
* Fix 2 typos by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/62
* Propagate `doc` field to abstract CWL format by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/65
* Linting fixes by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/64
* Maintain collection_type if present by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/68
* Fix schema doc build by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/69
* Lint and deprecation fixes by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/70
* Run java codegenerator by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/71
* Run maven tests on pull_request by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/72
* fix schema-salad pycodegen by @mr-c in https://github.com/galaxyproject/gxformat2/pull/76
* Add workflow default file support by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/79
* Add typescript implementation by @mr-c in https://github.com/galaxyproject/gxformat2/pull/75
* Fix cytoscape HTML exports from dist package. by @jmchilton in https://github.com/galaxyproject/gxformat2/pull/82
* Add missing elements to schema, fix change_datatype conversion, CSS by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/83
* Support lists as data inputs by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/84
---------------------
0.15.0 (2020-08-12)
---------------------
* Lint types of default values.
* Fix bugs in schema related to differing type names between Galaxy and CWL.
* Generate cwl v1.2 instead of cwl v1.2.0-dev5 release now that it has been released.
* More testing of linting and CWL 1.2 export.
---------------------
0.14.0 (2020-08-11)
---------------------
* Bug fix where native export had explicit outputs declaration still in it (wouldn't break anything, but
was deceptive).
* Fixes for experimental CWL 1.2 abstract export.
* Improve script structures and documentation.
* Improve code structure - add more types, make more things immutable, mention mutability in docstrings.
---------------------
0.13.1 (2020-08-03)
---------------------
* Improve package structure - publish fixed sphinx docs, fix readme badges, add mypy typing support.
---------------------
0.13.0 (2020-07-30)
---------------------
* Add experimental export to CWL 1.2 using new abstract Operation classes.
---------------------
0.12.0 (2020-07-27)
---------------------
* Drop support for Python 2 - to support next bullet.
* Update schema parser for recent changes to schema salad.
---------------------
0.11.4 (2020-07-27)
---------------------
* Added abstraction for uniform access to workflow outputs across formats.
---------------------
0.11.3 (2020-07-23)
---------------------
* Bug fixes for exporting newer input concepts from native to Format 2.
* Added abstraction for uniform access to workflow inputs across formats.
---------------------
0.11.2 (2020-07-22)
---------------------
* Rework cytoscape and helpers for reuse from Planemo.
* Rev markdown validator for and from latest Galaxy changes.
---------------------
0.11.1 (2020-02-25)
---------------------
* Bug fix for gxwf-lint invocation from setup.py installed script.
---------------------
0.11.0 (2020-02-25)
---------------------
* Validate Galaxy Markdown in workflow reports as part of linting.
* Improved null handling in native ga workflow linting.
* Enhancements to workflow linting from Python. Lint for lack of documentation,
tools using the test toolshed, and implement special linting for training
material workflows to ensure a tag matches the workflow topic.
* Add gxwf-viz script that produces a cytoscape visualization of a workflow.
---------------------
0.10.1 (2019-12-07)
---------------------
* Bug fix to handle outputs without labels in Format 2 - they
don't validate per se but they are important for testing in the
Galaxy framework.
---------------------
0.10.0 (2019-12-06)
---------------------
* Implement scheam, validation, linting (for Format 2 and .ga).
* Handle new reports field in Galaxy 19.09 workflows.
* Numerous fixes for conversiion to and from native workflows.
* Numerous new test cases.
* Implement Java project for valiating and linting both kinds of workflows.
---------------------
0.9.0 (2019-07-08)
---------------------
* Implement default values in gxformat2.
---------------------
0.8.4 (2019-06-24)
---------------------
* Fix output IDs of 0.
---------------------
0.8.3 (2019-05-23)
---------------------
* Implement set_columns PJA.
---------------------
0.8.2 (2019-03-16)
---------------------
* Allow another API return option for experimental tool creation API.
---------------------
0.8.1 (2019-03-11)
---------------------
* Implement change datatype PJA.
---------------------
0.8.0 (2018-11-01)
---------------------
* Implement experimental CWL-style step defaults (see Galaxy PR #6850).
---------------------
0.7.1 (2018-10-09)
---------------------
* Various small fixes for changes in 0.7.1.
---------------------
0.7.0 (2018-10-08)
---------------------
* Add some basic test cases.
* Allow ID-map style listing of steps.
* Ordered load (in addition to existing dump functionality) or ordering of steps in ID-map style variant works.
* Allow CWL-style $graph defs that can define multiple workflows in a single file.
* Initial work on de-duplicating subworkflow definitions on import.
* Fix position handling while exporting workflow.
---------------------
0.6.1 (2018-10-01)
---------------------
* Fix export of non-data parameters and implicit workflow connections.
---------------------
0.6.0 (2018-10-01)
---------------------
* Various fixes, allow id map style workflow input definitions.
---------------------
0.5.0 (2018-10-01)
---------------------
* More fixes for PJA, add the ``doc`` keyword to format 2 workflows to match CWL workflows. Map to and from native Galaxy workflows as annotations.
---------------------
0.4.0 (2018-10-01)
---------------------
* Fixes for exporting PJA when exporting workflows from native .ga to format 2.
---------------------
0.3.2 (2018-10-01)
---------------------
* Fixes for exporting workflow outputs from native .ga to format 2, support for modern map style output definitions like CWL 1.0.
---------------------
0.3.1 (2018-10-01)
---------------------
* Fixes for exporting subworkflows from native .ga to format 2.
---------------------
0.3.0 (2018-09-30)
---------------------
* More cwl style inputs, initial work on conversion from native workflows, various small fixes and tweaks.
---------------------
0.2.0 (2018-02-21)
---------------------
* Bring in latest Galaxy updates - Python 3 fixes, safe YAML usage, and more PJA implemented.
---------------------
0.1.1 (2016-08-15)
---------------------
* Fix one Python 3 incompatibility.
---------------------
0.1.0 (2016-05-02)
---------------------
* Initial version - code from Galaxy's test framework with changes
based on planemo testing.
.. github_links
.. _Pull Request 99: https://github.com/galaxyproject/gxformat2/pull/99
.. _Pull Request 98: https://github.com/galaxyproject/gxformat2/pull/98
.. _Pull Request 96: https://github.com/galaxyproject/gxformat2/pull/96
.. _Pull Request 94: https://github.com/galaxyproject/gxformat2/pull/94
.. _Pull Request 95: https://github.com/galaxyproject/gxformat2/pull/95
.. _Pull Request 92: https://github.com/galaxyproject/gxformat2/pull/92
.. _Pull Request 90: https://github.com/galaxyproject/gxformat2/pull/90
.. _@mvdbeek: https://github.com/mvdbeek
.. _@mr-c: https://github.com/mr-c
.. _@nsoranzo: https://github.com/nsoranzo
.. _@jmchilton: https://github.com/jmchilton
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"description": "\n.. image:: https://readthedocs.org/projects/gxformat2/badge/?version=latest\n :target: https://gxformat2.readthedocs.io/en/latest/\n\n.. image:: https://badge.fury.io/py/gxformat2.svg\n :target: https://pypi.python.org/pypi/gxformat2/\n\n.. image:: https://github.com/galaxyproject/gxformat2/workflows/Python%20CI/badge.svg\n :target: https://github.com/galaxyproject/gxformat2/actions?query=workflow%3A%22Python+CI%22\n\n.. image:: https://github.com/galaxyproject/gxformat2/workflows/Java%20CI/badge.svg\n :target: https://github.com/galaxyproject/gxformat2/actions?query=workflow%3A%22Java+CI%22\n\n.. image:: https://img.shields.io/badge/latest%20schema-v19.09-blue\n :target: https://galaxyproject.github.io/gxformat2/v19_09.html\n\nFormat 2\n--------\n\nThis package defines a high-level Galaxy_ workflow description termed \"Format\n2\". The current schema version is v19_09 and the schema can be found\n`here <https://galaxyproject.github.io/gxformat2/v19_09.html>`__. This version of\nworkflow format can be consumed by Galaxy since version 19.09.\n\nThe Format 2 workflow description is still somewhat experimental and may\nyet change in small potentially backward incompatible ways until the format is\nexported by Galaxy by default.\n\nThe traditional Galaxy workflow description (files ending in ``.ga`` extension,\nsometimes called native workflows in this project) was not designed to be\nconcise and is neither readily human readable or human writable. Galaxy\nworkflow Format 2 is being designed to address these limitations,\nwhile also moving Galaxy's workflow description language toward standards such\nas the Common Workflow Language.\n\ngxformat2\n---------\n\nThis Python project can be installed from PyPI using ``pip``.\n\n::\n\n $ pip install gxformat2\n\nCheckout the project tests or how it used in projects such as Planemo and\nGalaxy to see how to use the gxformat2 library. Reference documentation for\nthe `modules <https://gxformat2.readthedocs.io/en/latest/py-modindex.html>`__\ncan be found as part of the project's documentation.\n\nThis project also includes various scripts for working with Galaxy workflows.\nCheckout their help for more information.\n\n::\n\n $ gxwf-lint --help\n $ gxwf-viz --help\n $ gxwf-abstract-export --help\n\nThis library and associated scripts are licensed under the MIT License.\n\n.. _Galaxy: https://galaxyproject.org/\n\n\n\n\nHistory\n-------\n\n.. to_doc\n\n---------------------\n0.19.0 (2024-07-23)\n---------------------\n* Sync markdown_parse with Galaxy (thanks to `@mvdbeek`_). `Pull Request 99`_\n* More helpers for reasoning about gxformat2 steps (thanks to `@jmchilton`_).\n `Pull Request 98`_\n* Add abstraction for popping connection dictionary to model (thanks to\n `@jmchilton`_). `Pull Request 96`_\n* Add now mandatory readthedocs config files (thanks to `@nsoranzo`_). `Pull\n Request 94`_\n* Use `ConnectedValue` for connected values (thanks to `@mvdbeek`_). `Pull\n Request 95`_\n* Refresh codegen using schema-salad 8.4.20230808163024 (thanks to `@mr-c`_).\n `Pull Request 92`_\n* Update label comment (thanks to `@mvdbeek`_). `Pull Request 90`_\n\n---------------------\n0.18.0 (2023-05-12)\n---------------------\n* Fix input conversion if input has no label by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/89\n\n---------------------\n0.17.0 (2023-01-06)\n---------------------\n\n* Enable \"when\" for workflow steps by @mr-c in https://github.com/galaxyproject/gxformat2/pull/74\n* When fixes by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/86\n\n---------------------\n0.16.0 (2022-09-20)\n---------------------\n\n* Add dev ``when`` on steps to backend (don't expose in schema yet). by @jmchilton in https://github.com/galaxyproject/gxformat2/pull/48\n* Update project plumbing to allow dev release. by @jmchilton in https://github.com/galaxyproject/gxformat2/pull/49\n* Drop support for Python 3.5, add 3.9 by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/52\n* Relicense under the MIT license by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/58\n* Format2: Add `label` attribute to `WorkflowInputParameter` and `WorkflowOutputParameter` by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/56\n* Misc fixes and refactorings by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/55\n* Convert Format2 workflow `label` to native `name` by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/54\n* test_abstract_export: use different names for the different outputs by @simleo in https://github.com/galaxyproject/gxformat2/pull/57\n* Fix 2 typos by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/62\n* Propagate `doc` field to abstract CWL format by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/65\n* Linting fixes by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/64\n* Maintain collection_type if present by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/68\n* Fix schema doc build by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/69\n* Lint and deprecation fixes by @nsoranzo in https://github.com/galaxyproject/gxformat2/pull/70\n* Run java codegenerator by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/71\n* Run maven tests on pull_request by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/72\n* fix schema-salad pycodegen by @mr-c in https://github.com/galaxyproject/gxformat2/pull/76\n* Add workflow default file support by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/79\n* Add typescript implementation by @mr-c in https://github.com/galaxyproject/gxformat2/pull/75\n* Fix cytoscape HTML exports from dist package. by @jmchilton in https://github.com/galaxyproject/gxformat2/pull/82\n* Add missing elements to schema, fix change_datatype conversion, CSS by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/83\n* Support lists as data inputs by @mvdbeek in https://github.com/galaxyproject/gxformat2/pull/84\n\n\n---------------------\n0.15.0 (2020-08-12)\n---------------------\n\n* Lint types of default values.\n* Fix bugs in schema related to differing type names between Galaxy and CWL.\n* Generate cwl v1.2 instead of cwl v1.2.0-dev5 release now that it has been released.\n* More testing of linting and CWL 1.2 export.\n\n---------------------\n0.14.0 (2020-08-11)\n---------------------\n\n* Bug fix where native export had explicit outputs declaration still in it (wouldn't break anything, but\n was deceptive).\n* Fixes for experimental CWL 1.2 abstract export.\n* Improve script structures and documentation.\n* Improve code structure - add more types, make more things immutable, mention mutability in docstrings.\n\n---------------------\n0.13.1 (2020-08-03)\n---------------------\n\n* Improve package structure - publish fixed sphinx docs, fix readme badges, add mypy typing support.\n\n---------------------\n0.13.0 (2020-07-30)\n---------------------\n\n* Add experimental export to CWL 1.2 using new abstract Operation classes.\n\n---------------------\n0.12.0 (2020-07-27)\n---------------------\n\n* Drop support for Python 2 - to support next bullet.\n* Update schema parser for recent changes to schema salad.\n\n---------------------\n0.11.4 (2020-07-27)\n---------------------\n\n* Added abstraction for uniform access to workflow outputs across formats.\n\n---------------------\n0.11.3 (2020-07-23)\n---------------------\n\n* Bug fixes for exporting newer input concepts from native to Format 2.\n* Added abstraction for uniform access to workflow inputs across formats.\n\n---------------------\n0.11.2 (2020-07-22)\n---------------------\n\n* Rework cytoscape and helpers for reuse from Planemo.\n* Rev markdown validator for and from latest Galaxy changes.\n\n---------------------\n0.11.1 (2020-02-25)\n---------------------\n\n* Bug fix for gxwf-lint invocation from setup.py installed script.\n\n---------------------\n0.11.0 (2020-02-25)\n---------------------\n\n* Validate Galaxy Markdown in workflow reports as part of linting.\n* Improved null handling in native ga workflow linting.\n* Enhancements to workflow linting from Python. Lint for lack of documentation,\n tools using the test toolshed, and implement special linting for training\n material workflows to ensure a tag matches the workflow topic.\n* Add gxwf-viz script that produces a cytoscape visualization of a workflow.\n\n---------------------\n0.10.1 (2019-12-07)\n---------------------\n\n* Bug fix to handle outputs without labels in Format 2 - they\n don't validate per se but they are important for testing in the\n Galaxy framework.\n\n---------------------\n0.10.0 (2019-12-06)\n---------------------\n\n* Implement scheam, validation, linting (for Format 2 and .ga).\n* Handle new reports field in Galaxy 19.09 workflows.\n* Numerous fixes for conversiion to and from native workflows.\n* Numerous new test cases.\n* Implement Java project for valiating and linting both kinds of workflows.\n\n---------------------\n0.9.0 (2019-07-08)\n---------------------\n\n* Implement default values in gxformat2.\n\n---------------------\n0.8.4 (2019-06-24)\n---------------------\n\n* Fix output IDs of 0.\n\n---------------------\n0.8.3 (2019-05-23)\n---------------------\n\n* Implement set_columns PJA.\n\n---------------------\n0.8.2 (2019-03-16)\n---------------------\n\n* Allow another API return option for experimental tool creation API.\n\n---------------------\n0.8.1 (2019-03-11)\n---------------------\n\n* Implement change datatype PJA.\n\n---------------------\n0.8.0 (2018-11-01)\n---------------------\n\n* Implement experimental CWL-style step defaults (see Galaxy PR #6850).\n\n---------------------\n0.7.1 (2018-10-09)\n---------------------\n\n* Various small fixes for changes in 0.7.1.\n\n---------------------\n0.7.0 (2018-10-08)\n---------------------\n\n* Add some basic test cases.\n* Allow ID-map style listing of steps.\n* Ordered load (in addition to existing dump functionality) or ordering of steps in ID-map style variant works.\n* Allow CWL-style $graph defs that can define multiple workflows in a single file.\n* Initial work on de-duplicating subworkflow definitions on import.\n* Fix position handling while exporting workflow.\n\n---------------------\n0.6.1 (2018-10-01)\n---------------------\n\n* Fix export of non-data parameters and implicit workflow connections.\n\n---------------------\n0.6.0 (2018-10-01)\n---------------------\n\n* Various fixes, allow id map style workflow input definitions.\n\n---------------------\n0.5.0 (2018-10-01)\n---------------------\n\n* More fixes for PJA, add the ``doc`` keyword to format 2 workflows to match CWL workflows. 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