mvdbeek
962839d68d
Merge branch 'release_24.1' into release_24.2
2024-12-20 11:19:12 +01:00
Marius van den Beek and Nicola Soranzo
d66555ec1e
...
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2024-12-19 16:54:03 +01:00
Marius van den Beek
5c2a471afa
Fix branch reference
2024-12-19 15:47:09 +01:00
mvdbeek
02492685cc
Use select_from_url test data from github, not usegalaxy.org
2024-12-19 14:14:05 +01:00
John Davis
8cdd25470a
Merge branch 'release_24.1' into dev
2024-11-20 00:15:54 -05:00
mvdbeek
974d7e58bf
Tighten conversion target input
...
This way we test that conversion to txt occurs via fasta, not the fasta
to tabular converter.
2024-11-19 17:33:58 +01:00
davelopez
2bdcec0dda
Add test for gx_allow_uri_if_protocol with deferred collections
2024-11-03 12:47:15 +01:00
davelopez
605389f1f2
Expand documentation on allow_uri_if_protocol
2024-11-03 11:06:25 +01:00
davelopez
678caa415f
Add test for allow_uri_if_protocol with deferred input
2024-10-31 11:17:17 +01:00
John Chilton
730ea2ee03
Pydantic models for parameter validators.
2024-10-22 07:49:37 -04:00
John Chilton
951ab47f47
More tool tests.
2024-10-22 07:49:37 -04:00
Dannon
9e01e37bc1
Merge pull request #18891 from kostrykin/multi-channel-images/dev
...
Add support for arbitrarily ordered image axes in image content assertions
2024-10-04 11:40:37 -04:00
mvdbeek
b02f46b1f4
Implement filter null database operation tool
2024-10-02 20:02:01 +02:00
John Chilton
ad73e9e838
Tool Request models.
2024-09-30 13:25:02 -04:00
John Chilton
b367c8a5a3
More tests for various data column feature combos.
2024-09-30 13:25:02 -04:00
mvdbeek
3f39b62eed
Merge branch 'release_24.1' into dev
2024-09-30 16:08:29 +02:00
mvdbeek
b5d46aa943
Test workflow module building with dynamic parameters
...
and parameter references and validators.
2024-09-30 13:48:03 +02:00
Leonid Kostrykin
9e26ada12b
Merge branch 'dev' into multi-channel-images/dev
2024-09-25 18:36:06 +02:00
Leonid Kostrykin
6a6a954998
Add slice attribute for image content-based assertions
2024-09-25 18:26:12 +02:00
Leonid Kostrykin
bd501713c7
Add frame attribute for image content-based assertions
2024-09-25 18:13:49 +02:00
Leonid Kostrykin
371264ca90
Add test for TYX axes
2024-09-25 18:02:05 +02:00
Leonid Kostrykin
95ab2cad17
Add has_image_depth assertion
2024-09-25 17:32:30 +02:00
Leonid Kostrykin
253b550e15
Add test for ZYX axes
2024-09-25 17:11:26 +02:00
Leonid Kostrykin
1050983124
Add test for ZCYX axes
2024-09-25 16:59:32 +02:00
Leonid Kostrykin
0bf9266627
Add support for YXCS axes in asserts/image.py
2024-09-25 13:21:47 +02:00
John Chilton
675c9670e2
Models for YAML test format.
2024-09-24 12:47:07 -04:00
John Chilton
0863221237
Merge pull request #18743 from jmchilton/parameter_models_rework_test_case_xml
...
Improvements to parameter models for test case inputs
2024-09-19 11:02:56 -04:00
John Chilton
67b4a69c1b
Merge pull request #18722 from jmchilton/markdown_help_2
...
Improvements to help terms & tool help.
2024-09-03 12:41:05 -04:00
John Chilton
10ef0a0203
Fix stray xml attribute that does nothing.
2024-08-26 16:55:48 -04:00
John Chilton
7b294fcaaa
Implement tool upgrade assistant script.
...
Inspect a tool's XML file and provide advice on upgrading to new tool versions. It is implemented as a library in tool_util for integration with Planemo in the future but I've added a script here to run it on the command-line directly. It can also output in JSON for integration with external tools such as the galaxy language server.
2024-08-24 11:22:43 -04:00
John Chilton
701c6f552d
Improvements to help terms & tool help.
...
- Allow tools to declare markdown help.
- Allow tools to reference help terms from their Markdown tools.
- Auto generate help terms for each datatype from values in datatypes_conf.xml
- Add permenant links for each help term - both the auto generated ones and the YAML specified
ones.
- Add some initial help terms for collection operations.
- Use new help term for "map over" from tool form.
2024-08-23 11:03:13 -04:00
John Chilton
0a35eea309
Tool test case parameter models.
2024-08-23 09:46:44 -04:00
John Chilton
e475003830
Disable unqualified parameters in test cases for new tools.
2024-08-23 09:46:44 -04:00
John Chilton
b919f21c47
Parameter models for optional data columns.
2024-08-11 17:19:21 -04:00
John Chilton
67dc43f4e1
Parameter models for multiple=true data column data parameters.
2024-08-11 17:19:21 -04:00
John Chilton
c6ea4d3dff
More clarification of empty/multiple/optional select behaviors.
2024-08-11 17:19:21 -04:00
John Chilton
95da14738e
Parmaeter models for multiple=true group tags.
2024-08-11 17:19:21 -04:00
John Chilton
c18bfa3475
Tool parameter models for optional group tags.
2024-08-10 10:30:20 -04:00
John Chilton
483df0c53f
Cleanup a test tool copy-pasta
2024-08-09 12:47:55 -04:00
John Chilton
ed720332b9
Parameter models for directory_uri parameters.
2024-08-09 11:54:19 -04:00
John Chilton
aa569ae71b
Parameter models for genomebuild parameters
2024-08-09 11:54:19 -04:00
John Chilton
53a1ee520f
Update parameter models for required integers.
2024-08-09 11:54:19 -04:00
John Chilton
01292d96e3
Fix more test case errors caught by parameter validation.
2024-08-09 11:54:19 -04:00
John Chilton
e530227ac6
Implement group tag testing in tools.
2024-08-09 11:54:19 -04:00
John Chilton
27ecea0bfc
Address PR comment in gx_select.xml, improve comment.
2024-08-09 11:54:19 -04:00
mvdbeek
5f635a3917
Merge branch 'release_24.1' into dev
2024-08-07 12:59:25 +02:00
Marius van den Beek
f8175ef771
Merge pull request #18552 from dannon/update-h5web
...
[24.1] Update h5web
2024-08-06 18:00:56 +02:00
John Chilton
e8e569f820
Work toward data column support in tool parameter meta models.
2024-08-05 18:37:24 -04:00
John Chilton
c92f6dd47c
Richer typing / models / parsing for drill down parameters.
2024-08-05 17:02:51 -04:00
Dannon Baker
ab90c943ff
Load h5 datatype in reduced test datatypes set
2024-08-05 10:58:22 -04:00
mvdbeek