Daniela Schneider
ff43229f3c
Update label for invert parameter in grep.xml
2026-04-23 10:44:34 +02:00
thepineapplepirate
db934422d8
updated qiskit interactive tool
2026-02-27 14:52:07 -05:00
Wolfgang Maier
e5027b0f5b
Revert all version bumps
2026-01-23 12:15:01 +01:00
Wolfgang Maier
5575d4ea0e
Disable input pattern sanitization in grep tool
2026-01-23 11:23:42 +01:00
Nicola Soranzo
17003e8d00
Apply 2026 black style
2026-01-20 10:25:45 +00:00
Bjoern Gruening
1805f26df8
add new jupter version
2026-01-04 11:36:24 +01:00
mvdbeek
c983e448a9
Set profile version for shipped expression tools
2025-10-23 15:51:30 +02:00
mvdbeek
003cf64326
Fix comp1 / test_subworkflow_map_over_data_column
2025-10-01 16:05:01 +02:00
Marius van den Beek
875278cafa
Merge pull request #20840 from natefoo/modernize-tools
...
Modernize tools in the filters/ dir
2025-10-01 11:07:40 +02:00
mvdbeek
b85262d86f
Skip set -e
2025-10-01 09:57:10 +02:00
Marius van den Beek
5feec4a139
Merge pull request #20692 from bgruening/it-rstudio-bams
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Add special case for BAM files in RStudio
2025-10-01 09:44:49 +02:00
mvdbeek
657b9f7f6c
Add separate out file for MAF_Limit_To_Species1 test
...
The test file is shared with MAF_filter, so if you use the same file
only one of the tests can pass.
2025-09-26 12:47:24 +02:00
Nate Coraor
7a88000aff
Update maf tools with profiles, required_files, and requirements.
2025-09-25 18:13:26 +02:00
mvdbeek
b95faeac05
Change grep test pattern and restore assertions
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addresses https://github.com/galaxyproject/galaxy/pull/20840/files#r2345064008
2025-09-25 17:56:35 +02:00
Nate Coraor
585392b367
Add missing stuff pointed out in code review
2025-09-25 17:40:08 +02:00
Nate Coraor
0e8c2a0af5
Tool profiles and required_files
2025-09-25 17:38:39 +02:00
Nate Coraor
7a06cd5c1e
Set tool profile and update dep version of join1
2025-09-25 17:38:39 +02:00
Nate Coraor
41441c5d0d
Drop comp1 python wrapper and modernize
2025-09-25 17:38:38 +02:00
Nate Coraor
25eb8a3248
Modernize more tools in filters/
2025-09-25 17:38:37 +02:00
Nate Coraor
a6ce6519b6
Add coreutils requirement to cat1
2025-09-25 17:38:37 +02:00
Nate Coraor
ddee579f7c
Add required_files
2025-09-25 17:38:36 +02:00
Nate Coraor and Björn Grüning
393a6e07b2
Apply suggestions from code review
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Co-authored-by: Björn Grüning <bjoern@gruenings.eu >
2025-09-25 17:38:36 +02:00
Nate Coraor
5f77bb55ed
Modernize Remove Beginning1, drop perl wrapper
2025-09-25 17:38:35 +02:00
Nate Coraor
e08d37f10d
Modernize Paste1, drop perl wrapper
2025-09-25 17:38:35 +02:00
Nate Coraor
0ca869b65a
Modernize Convert characters1
2025-09-25 17:38:34 +02:00
Nate Coraor
7b2cf16c17
Modernize mergeCols1
2025-09-25 17:38:34 +02:00
Nate Coraor
e297e1efe4
Change cat1 name per wg-backend discussion
2025-09-25 17:38:33 +02:00
Nate Coraor
443c5cdd7c
Drop python wrapper for cat1, modernize
2025-09-25 17:38:31 +02:00
mvdbeek
f614ea290d
Generalize metadata file staging
2025-09-25 16:11:22 +02:00
Björn Grüning
117a793412
add special case for BAM files
2025-09-25 16:05:34 +02:00
Nicola Soranzo
857948c033
Update requirements of sort1 tool
...
Otherwise the conda environment for it fails to solve with the following
error:
```
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- package grep-2.14-h470a237_2 is excluded by strict repo priority
```
This is due to the fact that grep 2.14 is only available on the bioconda
channel, while newer versions are on conda-forge, which has a higher
priority.
Reported by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20876/files#r2336209775 .
2025-09-11 01:44:30 +01:00
Nicola Soranzo
26e6a17a17
Fix skipping of empty lines in gtf_filter_by_attribute_values_list tool
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Introduced in https://github.com/galaxyproject/galaxy/pull/11365 .
2025-09-10 03:45:54 +01:00
Nicola Soranzo
bafa6de88e
Fix incorrect test for Grep1 tool
2025-09-10 03:22:09 +01:00
Nicola Soranzo
eb0a33ff39
Fix gff_filter_by_attribute and gff_filter_by_feature_count tools for recent Python
...
Original fix by @natefoo in
https://github.com/galaxyproject/galaxy/pull/20840 .
2025-09-10 03:21:14 +01:00
Nicola Soranzo
0abc2f7d97
Fix ldtools if tool path contains spaces
2025-09-10 02:14:50 +01:00
Nicola Soranzo
4768d3d1db
Drop Python helper script from sort1 tool
...
Also:
- Incidentally address the deprecation of the `argparse.FileType` type
converter in Python 3.14 , see
https://docs.python.org/3.14/whatsnew/3.14.html#deprecated
https://github.com/galaxyproject/galaxy/issues/16854
- Drop the now unnecessary Python requirement.
- Use CDATA.
2025-09-08 23:47:46 +01:00
mvdbeek
30af8fb6ea
Merge branch 'release_25.0' into dev
2025-08-29 20:00:19 +02:00
mvdbeek
4225e4b0fa
Merge branch 'release_24.2' into release_25.0
2025-08-29 19:59:33 +02:00
mvdbeek
541d70acf6
Include galaxy user agent in data source tools
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Closes https://github.com/galaxyproject/galaxy/issues/20833
2025-08-29 17:22:28 +02:00
Björn Grüning
a08f04e5e1
Merge branch 'dev' into cleaner_wording
2025-06-12 22:55:03 +02:00
Enis Afgan
dc248bb980
Add icons for many ITs
2025-05-12 10:07:25 -04:00
Dannon Baker
3bf1e0400e
Add a set of logos for interactive tools
2025-05-12 10:07:24 -04:00
Dannon Baker
312c134493
Square-ify jupyter logo
2025-05-12 10:07:24 -04:00
Dannon Baker
452f3e402c
Logo for jupyter notebook
2025-05-12 10:07:24 -04:00
Björn Grüning
46c35f3234
Merge branch 'dev' into cleaner_wording
2025-04-27 09:03:08 +02:00
Nate Coraor
cf1333a148
Also chown R lib in RStudio BioC tool
2025-04-16 11:39:38 -04:00
Nate Coraor
9e43a5788d
Merge pull request #19924 from afgane/rstudio32
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RStudio IT updates to work on .org
2025-04-10 10:11:39 -04:00
Daniel Blankenberg
491f415173
Merge pull request #19689 from jaidevjoshi83/DICED
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Data-source tool for DICED database (https://diced.lerner.ccf.org/ ) added.
2025-04-09 15:33:49 -04:00
Björn Grüning
bedf19baa4
change description of the export tool
2025-04-05 22:25:22 +02:00
mvdbeek
b0c197c9e6
Drop unnecessary global statements
2025-04-05 09:55:42 +02:00
Daniela Schneider