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14 Commits
Author SHA1 Message Date
mvdbeek 73dc126e67 Use format_source="input" instead of format="input" 
Fixes https://github.com/galaxyproject/galaxy/issues/15302
 2023-01-13 10:58:57 +01:00
mvdbeek 350508909d Fix more tests 
Include a perl dependency and profile version for the `addValue` tool.
It otherwise fails on OSX with
```
INFO     galaxy.tool_util.output_checker:output_checker.py:155 Job failed because of contents in the standard error stream: [perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
	LC_ALL = (unset),
	LC_CTYPE = "C.UTF-8",
	LANG = (unset)
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
]
```

Also fix CollectionTypeDescription when collection_type is already CollectionTypeDescription
and fix some wrong type annotations in lib/galaxy/tools/actions/__init__.py

Into more fixes
 2022-11-09 15:35:31 +01:00
Helena Rasche 646b133bb3 Add EDAM topics to unannotated tools 2020-10-30 17:59:45 +01:00
Dannon Baker b652159963 Fix ancient typo in fixedValueColumn tool. 2019-09-26 16:08:55 -04:00
Nicola Soranzo f865e8359f Deprecate size attribute of <param/> and remove it from tools 
Also:
- dos2unix test/functional/tools/for_workflows/head.xml
- Single-quote text and data params in `<command/>`
- Remove deprecated `interpreter` attribute of `<command />`
 2018-09-10 11:34:37 +01:00
peterjc fce2184e5b Make tool version explicit (Job runner would assume 1.0.0) 2015-03-09 15:21:48 +00:00
Dave Bouvier 576ceb7829 Revert tool migration. 2012-12-07 16:38:26 -05:00
Dave Bouvier de7cb21382 Migrate tools to tool shed: addValue, ChangeCase, Condense characters1, Convert characters1, Cut1, mergeCols1, Remove beginning1, Show beginning1, Show tail1, trimmer 2012-12-07 16:08:40 -05:00
Dannon Baker 349d3a07bb First pass standardizing to 'dataaset' from 'query'. 2011-01-27 13:46:20 -05:00
Greg Von Kuster 69a20f0fa7 Corrected old directions on several tools. 2008-03-13 20:46:43 +00:00
Greg Von Kuster 4dd1f044e1 Removed tool version directiories for some of the tools...the rest soon. 2008-03-03 16:14:06 +00:00
Greg Von Kuster 32b40a5f27 Added more tool version directories for filters tool directoy. 2008-02-22 15:23:46 +00:00
Anton Nekrutenko 92d7aa70c5 interface and help edits for text manipulation tools 2007-07-31 21:24:24 +00:00
James Taylor f788a34fca Moving james-wsgi branch to new trunk. 2006-11-15 16:28:21 +00:00