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Overview

The Galaxy tool utilities.

History

26.1.1 (2026-08-04)

No recorded changes since last release

26.1.0 (2026-08-02)

Bug fixes

  • Avoid missing field value failure in data tables by @guerler in #21008

  • Escape `$` in galaxy.xsd to fix output filter docs rendering by @gdefazio in #21731

  • Fix ToolExpressionOutput.to_model() for boolean type by @jmchilton in #22007

  • Convert math.inf to None in JSON-serialized tool dicts by @dannon in #22152

  • Fix more paired_or_unpaired collection issues by @jmchilton in #22170

  • Fix mypy and packaging issues; pin rocrate<0.15.0 by @nsoranzo in #22469

  • Fix tool id handling for shed-installed tools by @guerler in #22553

  • Don’t install data table entries for non-DM tool installs by @natefoo in #22679

  • Harden access control for user-defined tools by @mvdbeek in #22704

  • [26.1 (spiritually)] Fix UDT collection outputs being silently dropped in YAML tool parser by @jmchilton in #22761

  • Relax legacy doi:-prefixed citation handling (#22795) by @mvdbeek in #22799

  • Add fixed color set from webcolors package by @guerler in #22869

  • Fix input mangling when conditional parameter name ends in `_N` by @mvdbeek in #22891

  • Always attempt to build tool request for new API endpoint by @mvdbeek in #22894

  • Accept dce collection references in the tool request model by @mvdbeek in #22926

  • Fix tool shed state serving for stock tools by @jmchilton in #22963

  • Make the user-defined tool schema robust for LLM authoring (CustomToolAgent) by @mvdbeek in #22968

  • Custom-tool agent: verified container resolution + authoring safeguards (with a reusable mulled-recommend CLI) by @mvdbeek in #22981

  • Fix celery worker cold-start thundering herd (build app once, scope tool-data walk to load pass) by @mvdbeek in #23048

  • Fix ToolPanelElements._section_by_tool being class-level shared state by @mvdbeek in #23062

  • Skip RST help linting when help format is not restructuredtext by @mvdbeek in #23073

  • Make verify_collection fail usefully on output-shape mismatches by @mvdbeek in #23134

  • Handle sample_sheet and paired_or_unpaired collections in output_to_cwl_json by @mvdbeek in #23152

Enhancements

  • Add support for test credentials in tools by @arash77 in #21643

  • Various YAML Tool Hardening and Progress toward Tool State Goals by @jmchilton in #21828

  • Migrate tool execution request from api/tools to api/jobs by @guerler in #21842

  • Add format_xml to galaxy-tool-util for shared XML formatting by @dannon in #21903

  • Converge framework workflow test syntax toward Planemo syntax by @jmchilton in #21907

  • Allow tools to specify time limits by @jmchilton in #21927

  • Eliminate Twill from Tool Shed tests by @jmchilton in #21953

  • Use ``os.path.join()`` or ``pathlib.Path`` instead of f-strings for filesystem paths by @nsoranzo in #21954

  • Migrate Python packages to `src` layout and pure namespace packages by @mr-c in #21977

  • Model subcollection mapping (map_over_type) and DCE in tool parameter schema by @jmchilton in #21991

  • Enrich tool parameter JSON Schema with Galaxy metadata via model methods by @mvdbeek in #22020

  • Replace mocked agent tests with static YAML backend for deterministic API/E2E testing by @jmchilton in #22070

  • Extend the favorite tool panel concept by @bgruening in #22212

  • Substantially expand tool form testing by @jmchilton in #22216

  • Restore the #22116 fixes that only apply to dev by @jmchilton in #22218

  • More Complete, Robust, and Tested JSON-Schema for Tool State Models by @jmchilton in #22362

  • Clean up Pydantic v2 deprecation warnings by @mvdbeek in #22463

  • Clean up remaining deprecation warnings by @mvdbeek in #22473

  • Narrow YAML schema by @jmchilton in #22507

  • Update Python dependencies by @galaxybot in #22559

  • Tighten the workflow test schema by @jmchilton in #22566

  • Add ``RetrySession`` to automatically retry idempotent HTTP requests by @nsoranzo in #22567

  • Push UserToolSource semantic validation onto the pydantic model by @mvdbeek in #22615

  • Update Python dependencies by @galaxybot in #22619

  • Expose more metadata in ParsedTool abstraction by @jmchilton in #22667

  • Add namespace stripping to ``CachedExplicitSingularityContainerResolver`` by @mvdbeek in #22878

  • Enforce color format in JSON schema tests via FormatChecker by @mvdbeek in #22909

Other changes

26.0.1 (2026-06-04)

Bug fixes

  • Fix testing, publishing and dependencies of packages by @nsoranzo in #22445

  • Accept bare ftype as valid test output check by @jmchilton in #22483

  • Fix data manager URL for managers with ‘+’ version suffix by @mvdbeek in #22525

26.0.0 (2026-04-08)

Bug fixes

  • When getting tool by uuid, get that exact tool by @mvdbeek in #21844

  • Fix Pydantic UnsupportedFieldAttributeWarning for Field defaults in Annotated by @mvdbeek in #21923

  • Backport paired or unpaired mapping fix by @mvdbeek in #21936

  • Fix ToolExpressionOutput.to_model() for boolean type. by @jmchilton in #22038

  • Model hidden_data params as optional data in tool meta-models. by @jmchilton in #22116

  • Fix validation of certain classes of text validators in tools. by @jmchilton in #22280

Enhancements

Other changes

  • Fix tool request API for multiple select parameters with defaults. by @jmchilton in #21416

25.1.2 (2026-03-09)

Bug fixes

25.1.1 (2026-02-03)

Bug fixes

  • Fix data manager .loc file selection logic by @jdavcs in #21664

Enhancements

Other changes

25.1.0 (2025-12-12)

Bug fixes

Enhancements

Other changes

25.0.4 (2025-11-18)

Bug fixes

25.0.3 (2025-09-23)

Bug fixes

  • Fix collection element sorting in extended_metadata by @mvdbeek in #20928

25.0.2 (2025-08-13)

Bug fixes

  • Fix restricting user defined tool input datasets extensions by @mvdbeek in #20545

  • Don’t fail volume mount construction for tools without tool directory by @mvdbeek in #20593

  • Input linter: add missing attribute to sort_by by @bernt-matthias in #20693

  • Fix test_base_image_for_targets mulled test to use mzmine by @nsoranzo in #20713

25.0.1 (2025-06-20)

Bug fixes

  • Fix single data element identifier to be a regular string by @mvdbeek in #20438

  • Relax validation of XML test assertion parsing by @mvdbeek in #20511

  • Fix import of galaxy.tool_util.cwl module by @nsoranzo in #20529

25.0.0 (2025-06-18)

Bug fixes

Enhancements

24.2.4 (2025-06-17)

Bug fixes

24.2.3 (2025-03-16)

Bug fixes

  • Fix parameter model constructions with leading underscores, fixes converter linting by @mvdbeek in #19790

24.2.2 (2025-03-08)

Bug fixes

Enhancements

  • Add bwa_mem2_index directory datatype, framework enhancements for testing directories by @mvdbeek in #19694

24.2.1 (2025-02-28)

Bug fixes

24.2.0 (2025-02-11)

Bug fixes

Enhancements

24.1.4 (2024-12-11)

Bug fixes

Enhancements

24.1.3 (2024-10-25)

Bug fixes

Enhancements

24.1.2 (2024-09-25)

Bug fixes

  • Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata by @nsoranzo in #18510

  • xsd: allow change_format and actions also in statically defined collection elements, and break recursion by @bernt-matthias in #18605

Enhancements

24.1.1 (2024-07-02)

Bug fixes

Enhancements

24.0.3 (2024-06-28)

Bug fixes

24.0.2 (2024-05-07)

Bug fixes

  • Tool linters: allow to skip by old linter names (by allowing to skip linter modules) by @bernt-matthias in #18091

  • tool linters: output filters should only consider child filter nodes by @bernt-matthias in #18096

24.0.1 (2024-05-02)

Bug fixes

24.0.0 (2024-04-02)

Bug fixes

Enhancements

Other changes

23.2.1 (2024-02-21)

Bug fixes

Enhancements

Other changes

23.1.4 (2024-01-04)

Bug fixes

  • Separate collection and non-collection data element by @mvdbeek in #17236

23.1.3 (2023-12-01)

No recorded changes since last release

23.1.2 (2023-11-29)

Bug fixes

  • Change log level for duplicate data table entries to warning by @mvdbeek in #16988

  • Upgrade minimum conda to be compatible with latest conda-build by @bernt-matthias in #17013

  • Fix duplicated tools in tool panel view section copying by @jmchilton in #17036

Enhancements

23.1.1 (2023-10-23)

Bug fixes

Enhancements

Other changes

23.0.6 (2023-10-23)

Bug fixes

  • Fixes for extra files handling and cached object stores by @mvdbeek in #16595

  • Fix create/install commands for conda 23.9.0 by @nsoranzo in #16831

23.0.5 (2023-07-29)

Bug fixes

23.0.4 (2023-06-30)

No recorded changes since last release

23.0.3 (2023-06-26)

Bug fixes

Enhancements

  • When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247

23.0.2 (2023-06-13)

Bug fixes

  • Don’t fail CWL tool parsing when Cheetah not installed by @mvdbeek in #16219

  • Allow skipping expect_num_outputs when expect_failure is set in tool test by @bernt-matthias in #16237

23.0.1 (2023-06-08)

Bug fixes

Enhancements

  • Allow setting auto_decompress property in staging interface by @mvdbeek in #16014

22.1.5 (2022-11-14)

  • Set test status to success on expected failure

22.1.4 (2022-10-28)

  • Add missing unittest_utils package to galaxy-tool-util

22.1.3 (2022-10-27)

  • Pin minimum pyopenssl version when installing Conda

  • Add --strict-channel-priority to conda create/install commands if using conda >=4.7.5

22.1.2 (2022-08-29)

  • Fix lint context error level

  • Pin galaxy-util to >= 22.1

  • Fix biocontainer resolution without beaker cache

22.1.1 (2022-08-22)

  • First release from the 22.01 branch of Galaxy

21.9.2 (2021-11-23)

  • Fix linting of multiple="true" select inputs.

21.9.1 (2021-11-03)

  • Fix tool linting.

21.9.0 (2021-11-03)

  • First release from the 21.09 branch of Galaxy.

21.1.2 (2021-06-23)

21.1.1 (2021-05-21)

21.1.0 (2021-03-19)

  • First release from the 21.01 branch of Galaxy.

20.9.1 (2020-10-28)

  • Bugfixes to work around & annotate expected tool test failures.

20.9.0 (2020-10-28)

  • First release from the 20.09 branch of Galaxy.

20.9.0.dev2 (2020-08-02)

  • First release from the 20.09 branch of Galaxy.

20.5.0 (2020-07-04)

  • First release from the 20.05 branch of Galaxy.

20.1.0 (2020-07-04)

  • First release from the 20.01 branch of Galaxy.

19.9.1 (2019-12-28)

  • Fix declared dependency problem with package.

19.9.0 (2019-12-16)

  • Initial import from dev branch of Galaxy during 19.09 development cycle.

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26.1.1 This release

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25.1.0

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25.0.4

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25.0.3

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25.0.2

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25.0.1

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25.0.0

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24.2.4

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24.2.3

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24.2.1

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24.2.0

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24.1.4

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24.1.3

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24.1.2

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24.0.3

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23.2.1

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23.1.2

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23.1.1

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23.0.6

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23.0.5

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23.0.4

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23.0.3

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23.0.2

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22.1.5

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22.1.4

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22.1.3

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22.1.2

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22.1.1

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21.9.2

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21.1.2

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21.1.1

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21.1.0

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20.9.1

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20.9.0

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19.9.1

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19.9.0

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