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2821 Commits
Author SHA1 Message Date
Marius van den Beek d8e261dbc2 Merge pull request #11859 from bernt-matthias/topic/grep-header 
grep, tail, head: add option to keep header
 2021-05-04 19:07:46 +02:00
Matthias Bernt a94b8816f6 Merge branch 'topic/grep-header' of https://github.com/bernt-matthias/galaxy into topic/grep-header 2021-05-04 15:00:19 +02:00
Matthias Bernt a45f06b881 fix test 3 and error detection 
only error for exit code > 1:
 2021-05-04 14:59:23 +02:00
M BerntandMarius van den Beek 181b862250 Apply suggestions from code review 
- add profile
- add requirement

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-05-04 13:47:29 +02:00
Matthias Bernt 85f643bc66 remove python wrapper for grep tool 
and fix cli (`-n +2`) for head, tail, grep
 2021-05-04 10:49:23 +02:00
Matthias Bernt 8cc1c3bc0f some updates for grep, tail, head 
- CDATA for all
- exit code
- remove interpreter
- bump versions
- and add the tools to WORKFLOW_SAFE_TOOL_VERSION_UPDATES
 2021-05-03 13:15:08 +02:00
John ChiltonandNicola Soranzo 652f700962 Update tools/extract/liftOver_wrapper.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-04-23 14:51:29 -04:00
John Chilton 2a0474730b Rev mypy. 2021-04-23 14:49:53 -04:00
mvdbeek f85086f6d5 Assert file:// urls are not being downloaded without explicit handling 
And allow file_sources in add_composite_file to_path
 2021-04-20 16:24:41 +02:00
Matthias Bernt d1e3edfb68 consider header in tail/head wrapper 
and remove pl wrapper
 2021-04-19 13:57:57 +02:00
Matthias Bernt fc3c6eef97 grep: add option to keep header 
https://github.com/galaxyproject/tools-iuc/issues/3511
 2021-04-18 22:18:14 +02:00
Matthias Bernt cfd0f02c56 add and use a new util foo is_url 2021-04-12 16:13:52 +02:00
Björn Grüning 393ce2f4fe small cleanups 2021-03-19 21:52:10 +01:00
Björn Grüning 96c943050c remove macros 2021-03-19 21:32:09 +01:00
Björn Grüning 77b8f3ee71 change tool ID 2021-03-19 09:05:33 +01:00
Marie Gramm 1f1344c3de change file name 2021-03-19 10:38:15 +11:00
Marie Gramm 76e7e2d4cf add license 2021-03-19 09:54:30 +11:00
Marie Gramm a7ff05a086 add interactive simtext tool, PR https://github.com/galaxyproject/tools-iuc/pull/3508 2021-03-13 10:55:13 +11:00
Nicola Soranzo 6c540932c7 Merge branch 'release_21.01' into dev 2021-03-12 19:01:35 +00:00
Anthony Bretaudeau b0fc281d54 Fix $HOME for some gxit requiring a specific one 2021-03-09 15:10:41 +01:00
Björn Grüning bfdd27ad89 bumping tool version 2021-03-05 14:47:32 -05:00
Bjoern Gruening 72805ef99c allow using OpenRefine without an input 2021-03-05 14:47:32 -05:00
Björn Grüning 9f31fe3e93 bump tool version 2021-03-05 14:47:32 -05:00
Björn Grüning 504e4d90ed fix spacing 2021-03-05 14:47:32 -05:00
Bjoern Gruening 2295368eae upgrade cellxgene container 2021-03-05 14:47:32 -05:00
Björn Grüning 4483861141 bump tool version 2021-03-05 14:47:32 -05:00
Bjoern Gruening a3dbd0c6c9 some pyiron fixes from EU 2021-03-05 14:47:31 -05:00
Marius van den Beek 5e763d1171 Merge pull request #11547 from bgruening/it_openrefine 
[21.01] allow using Openrefine without data inputs
 2021-03-05 13:45:28 +01:00
Marius van den Beek 768d1263a5 Merge pull request #11546 from bgruening/it_cellxgne 
[21.01] update the cellxgene IT container
 2021-03-05 13:45:11 +01:00
Björn Grüning 4172bacc75 bump tool version 2021-03-05 10:40:20 +01:00
Björn Grüning de9f787038 bump tool version 2021-03-05 10:39:42 +01:00
Björn Grüning e8d8fd837a bumping tool version 2021-03-05 10:39:07 +01:00
Bjoern Gruening 684c2bf436 allow using OpenRefine without an input 2021-03-05 10:24:03 +01:00
Björn Grüning 69d59614cb fix spacing 2021-03-05 10:19:54 +01:00
Bjoern Gruening 7d8b13daea upgrade cellxgene container 2021-03-05 10:16:11 +01:00
Bjoern Gruening ef5c9cd9e0 some pyiron fixes from EU 2021-03-05 09:55:20 +01:00
mvdbeek d6954bdd22 Merge branch 'release_21.01' into dev 2021-02-23 08:59:14 +01:00
mvdbeek 53ede0c2e4 Merge branch 'release_20.09' into release_21.01 2021-02-23 08:58:14 +01:00
mvdbeek a20919edaa Make hash selection mandatory 2021-02-22 11:13:02 +01:00
John Chilton f1ec1b6459 Merge pull request #11342 from mvdbeek/resolve_session_problems 
Resolve session problems, enabled pages and tags fastAPI routes
 2021-02-17 10:15:43 -05:00
Matthias Bernt 610e31147a add python requirement 2021-02-13 23:04:17 +01:00
Matthias Bernt 30fb1e2c2d Merge branch 'ccedmendoza_patch-1' of https://github.com/bernt-matthias/galaxy into ccedmendoza_patch-1 2021-02-13 22:03:16 +01:00
Matthias Bernt 4be9bc6430 bump tool version 2021-02-13 22:02:57 +01:00
M BerntandNicola Soranzo e4d9e1a29e Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-02-13 20:38:05 +01:00
Matthias Bernt faed88a1bd remove interpreter 2021-02-13 16:34:09 +01:00
Matthias Bernt cec6e6926b revert to a less intrusive change 2021-02-13 14:54:26 +01:00
ccedmendoza 765e700803 remove trailing white space 2021-02-13 14:47:24 +01:00
ccedmendoza 8491730b83 Corrent linting 2021-02-13 14:47:24 +01:00
ccedmendoza f44c0b311c Simplify script while adding empty lines and comments handling 2021-02-13 14:47:24 +01:00
ccedmendoza f9cf7e640c Make filter work with file containing header 2021-02-13 14:47:24 +01:00