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220 Commits
Author SHA1 Message Date
Nicola Soranzo b3dc7923db Python3: use collections.Mapping instead of removed DictMixin 2017-12-12 15:30:53 +00:00
M Bernt b2cc634e8a python3 fix (#5043) 
strings can not be written to byte mode file handlers.
writing resulted in: TypeError: a bytes-like object is required, not 'str'

Alternative would be to make string byte.
 2017-11-20 22:34:02 +01:00
Nicola Soranzo 9b4de72ca6 Fix all E722 errors and ignore E741 
Introduced in flake8 3.5.0
Fix import order.
 2017-10-24 11:29:09 +01:00
Nicola Soranzo 21b44bf348 Fix all E201 and E202 style errors 
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
 2017-08-17 11:35:39 +01:00
Nicola Soranzo 03a807e374 Lint some tools 2017-01-23 21:11:43 +00:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Daniel Blankenberg ba07956117 Fix tabular filtering tool broken in #2983 2016-10-13 10:40:40 -04:00
Nicola Soranzo 11b4f3a60c Fix import order and Python3 compatibility for tools/ 
xref #1715
 2016-09-29 19:26:22 +01:00
nturaga 4fabf51f4b typo in summary statistics tool 2016-07-20 15:27:24 -04:00
Gildas Le Corguillé f951249c79 Update gsummary.xml 
Delete r and rpy deps
 2016-07-12 13:28:42 +02:00
Gildas Le Corguillé e862067332 Update gsummary.xml 2016-07-07 16:41:06 +02:00
Gildas Le Corguillé f7cbefc1f3 Update gsummary.xml 
rpy seems not available within the Conda packages. 
So I add rpy2 in the requirements.

It works for me! I ❤️ Conda
 2016-07-07 12:02:51 +02:00
Timur Shtatland dba8d0bb0a Python3: tools/stats/aggregate_scores_in_intervals.py 2016-06-25 17:07:59 -04:00
Nicola Soranzo 1652e0ceed Add EDAM topics to tools and expose in API 2016-05-24 12:17:39 +01:00
Marius van den Beek c3ecd1eb72 Annotate tools with edam_operations 
to demonstrate usage of edam_operations in tool xml.
 2016-05-19 17:27:04 +02:00
Nicola Soranzo 6ba6f798ec Fix more E203 flake8 errors 2016-05-17 23:53:16 +01:00
Nicola Soranzo 8a43b2b492 Python 3: use "as" instead of comma in except clause 2016-05-17 23:53:16 +01:00
Nicola Soranzo ed4132d9c0 Python3: Use open() instead of file() 2016-05-17 23:53:16 +01:00
Daniel Blankenberg 34900f87f5 Fix grouping tool broken in 7347d75a4a / fd85979a86, and enhance performance when removing lines. 2016-04-14 12:00:11 -04:00
John Chilton 1f4b329032 Refactor galaxy.tools.exception_handling... 
... so datatype module doesn't need to import something from galaxy.tools - which causes a bunch of more things to be imported because galaxy.tools at the top-level has so many imports.
 2016-01-21 14:31:41 +00:00
John Chilton 2934c2f3bd Lint fix for 15.10 to dev merge. 2015-11-09 15:33:05 +00:00
John Chilton dc534bb258 Merge branch 'release_15.10' into dev 
Conflicts:
	client/galaxy/scripts/mvc/grid/grid-view.js
	static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
	static/scripts/mvc/collection/list-of-pairs-collection-creator.js
 2015-11-09 15:19:02 +00:00
Nicola Soranzo 69cda48690 Remove remaining references to galaxy.eggs . flake8 some files in tools/ . 2015-10-26 19:29:13 +00:00
Eric Enns 0ec1b17794 Update list comprehension to go through headings instead of summary so that we output in the order we want. 2015-10-14 08:28:30 -05:00
Eric Enns ad4458a458 Revert to previous changes if using rpy2 2015-10-09 10:34:20 -05:00
Eric Enns ad20452340 Fix output to print values and not hash key 2015-10-09 10:08:48 -05:00
Nate Coraor 6eafa52f41 Remove superflous assignment left over from 
647fcf1f60, thanks @nsoranzo.
 2015-07-13 14:55:33 -04:00
Nate Coraor 647fcf1f60 Only make the Group tool's return value an integer if rounding is 
selected, as pointed out by @nsoranzo.
 2015-07-13 11:01:55 -04:00
Oleksandr Moskalenko 58091b4b5b Make the Group tool return integer values when 'round to nearest integer' is selected 2015-07-04 17:58:07 +01:00
John Chilton 884e824d72 Merge remote-tracking branch 'vavrusa/table-datatype' into dev. 
Conflicts:
	lib/galaxy/datatypes/tabular.py
 2015-06-03 10:52:42 -04:00
Nicola Soranzo 22d4a1d8c3 dos2unix of tools/ directory. Some whitespace and PEP-8 fixes. 2015-05-15 12:40:52 +01:00
Björn Grüning 1dde01220c Remove plain R dependency 2015-04-29 21:49:04 +02:00
Marek Vavrusa e5aa966f1d stats/gsummary: RPy is deprecated, use RPy2/classic as an alternative 2015-04-29 17:24:22 +02:00
Björn Grüning 6f13a4be45 drop python-module 2015-04-29 16:47:37 +02:00
Björn Grüning e11e1864ef Update gsummary dependencies. 2015-04-29 12:14:07 +02:00
Dave Bouvier 35bc12d769 Migrate tools from the distribution to the tool shed. 2014-07-28 11:58:52 -04:00
John Chilton f8bf5f4d8e Merged in clayton_turner/galaxy-central (pull request #322) 
Added "ignore lines starting with specific characters" to group tool
 2014-02-20 10:35:58 -06:00
Dave Bouvier ba17a35a99 Remove stats/wiggle_to_simple, which is an exact duplicate of filters/wiggle_to_simple. 2014-02-14 12:34:58 -05:00
Clayton Turner fd85979a86 Fixed XML versioning and inputfile name 2014-02-14 12:25:20 -05:00
Clayton Turner 9e86f172bc Merge from stable 2014-02-10 16:49:43 -05:00
Clayton Turner 7347d75a4a Added ignore lines starting with specific characters to group tool 2014-02-10 16:00:30 -05:00
Daniel Blankenberg 3dbcdacfab Fix for aggregate_scores_in_intervals.py broken in 95bf71620d50c6d81248eef2001a7dc156ae1088. 2014-01-27 09:54:34 -05:00
John Chilton 4fb2b89347 White-list expressions executed by filtering and dna_filtering tools. 2013-11-04 14:55:00 -05:00
James Taylor d02155ad7b Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5 2013-04-09 11:57:38 -04:00
John Chilton 53cb37aed3 Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines. 
As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html).

There are still two copies.
 2013-11-07 12:56:48 -05:00
John Chilton 73206460d6 Backed out changeset 9532e80796ec 2013-11-07 13:02:22 -05:00
John Chilton 4a3820ef58 Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines. 
As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html).

There are still two copies.
 2013-11-07 12:56:48 -05:00
John Chilton be172fdfda Merge Pull Request #244. 2013-11-04 23:42:06 -06:00
Bjoern Gruening b172b602ad add [ and ] to mapped strings and advanced filters 2013-10-25 10:34:28 +02:00
Jeremy Goecks 502236ca2b Import clean up and documentation for compute tool. 2013-03-18 10:09:43 -04:00