John Chilton
54e8d22fa7
Check types of modules without type annotations in the their signatures on new modules.
...
https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-check-untyped-defs
> it type checks the body of every function, regardless of whether it has type annotations. (By default the bodies of functions without annotations are not type checked.)
2021-10-11 16:08:26 -04:00
Nicola Soranzo
d26b3d9848
Fix all E203, E741 and W504 flake8 errors
2021-01-18 10:35:41 +00:00
Nicola Soranzo
452aba9ee3
Fix remaining issues reported by bugbear; add it to flake8 reqs
2021-01-16 05:58:15 +00:00
Nicola Soranzo
9d74bba7fb
Drop support for retired Python 3.5
...
Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
2020-10-07 11:52:13 +01:00
Nicola Soranzo
739ab59eaa
Merge branch 'release_20.01' into dev
2020-02-20 00:23:19 +00:00
Nicola Soranzo
d4662fd952
Merge branch 'release_20.01' into dev
2020-02-19 12:43:07 +00:00
mvdbeek
a1fef39956
Adjust bx-python imports for https://github.com/bxlab/bx-python/commit/fd08da3b49e89e0accd2c372d4a99427628ce432
2020-02-19 10:53:24 +01:00
mvdbeek
05e8117995
Move aggregate_scores_in_intervals2 out of GALAXY_LIB_TOOLS_UNVERSIONED
2020-02-12 09:47:36 +01:00
mvdbeek
7d166eb24d
Bump version and add profile
2020-02-12 09:47:36 +01:00
mvdbeek
af4fdf7e1f
Drop __next__
2020-02-12 09:47:36 +01:00
mvdbeek
eac0ff9d7f
Fix vcf_to_maf_customtrack
2020-02-12 09:47:36 +01:00
Nicola Soranzo
f5cd88465e
Make str.join()s more efficient
...
by using generator expressions and tuples instead of lists.
2020-01-23 11:06:32 +00:00
Nicola Soranzo
d5a406cef7
Fix errors reported by new flake8 3.7.3
2019-01-31 13:47:21 +00:00
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
mvdbeek
36196bd2be
Specify maf ftype in maf_to_interval.xml
2018-09-05 14:22:01 +02:00
mvdbeek
aee261daf7
Fix random header order in MAF to FASTA
2018-09-05 14:22:01 +02:00
mvdbeek
e8d0ce39cf
Fix random order of fasta headers in maf_to_bed
2018-09-05 14:22:01 +02:00
mvdbeek
f22f0ebb2f
Sort maf_split_by_species test output
2018-09-05 14:22:01 +02:00
mvdbeek
548b9c8c89
Fix maf_to_bed.py
2018-09-05 14:22:00 +02:00
mvdbeek
2827dbf669
Fix maf_to_interval.py
2018-09-05 14:22:00 +02:00
mvdbeek
9949053f43
Fix maf_limit_to_species.py if no species is given
2018-09-05 14:22:00 +02:00
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
Nicola Soranzo
11b4f3a60c
Fix import order and Python3 compatibility for tools/
...
xref #1715
2016-09-29 19:26:22 +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
69cda48690
Remove remaining references to galaxy.eggs . flake8 some files in tools/ .
2015-10-26 19:29:13 +00:00
Nicola Soranzo
224d8f3fc4
Remove numpy requirement, not used since commit 09ce7a9b17 .
2015-05-15 12:41:08 +01:00
Nicola Soranzo
22d4a1d8c3
dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.
2015-05-15 12:40:52 +01:00
peterjc
fce2184e5b
Make tool version explicit (Job runner would assume 1.0.0)
2015-03-09 15:21:48 +00:00
John Chilton
4ddab82e9e
Add annotated citations for MAF tools.
...
Add macro file to centralize this and in help citation description as well.
2014-08-06 09:41:38 -04:00
Daniel Blankenberg
5e3e287ce3
Update MAF to BED to use job working directory and built-in primary dataset collection.
2014-04-18 13:23:38 -04:00
Daniel Blankenberg
213986aa7f
Update MAF to interval to use job working directory instead of __new_file_path__.
2014-04-18 12:34:08 -04:00
Nate Coraor
465b3ffc8d
Make maf-to-bed object-store aware
2013-03-06 12:40:31 -05:00
Jeremy Goecks
9a5679c37c
Use mako template in tool help so that dynamic image paths can be used. Fixes #141
2012-08-07 09:40:51 -04:00
Daniel Blankenberg
401d95cc73
MAF stats tool will now skip intervals with length less 1.
2011-09-23 09:36:57 -04:00
Daniel Blankenberg
378c5eeacd
Tool help updates.
2011-09-21 04:11:07 -04:00
Daniel Blankenberg
430b953cda
Minor tool help updates.
2011-08-25 10:00:09 -04:00
Daniel Blankenberg
1dfdc42fe6
Update tool help for some MAF tools.
2011-05-17 12:07:25 -04:00
Daniel Blankenberg
4eb1b0a79f
Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
2011-02-28 12:16:28 -05:00
Kanwei Li
2d0b8eb830
Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141
2010-12-14 14:22:13 -05:00
James Taylor
6b95a1f7fd
Automated merge with https://bitbucket.org/galaxy/galaxy-central/
2010-08-04 14:01:39 -04:00
Kanwei Li
a1f9e6a572
Support for VCFv4.0 and misc VCF fixes [Brad Chapman]
...
- Support for VCFv4.0, which should be identical to 3.3 support
- Correctly handle chromosome references when they start with 'chr' (instead of just numbers)
- Handle extra empty tabs on the header line which are present in GATK produced VCF and confuse the determination of how many sample states should be parsed.
2010-08-03 10:43:32 -04:00
Daniel Blankenberg
5461c97a7b
Update vcf_to_mafcustomtrack tool to enforce a minimum of one dataset to be selected.
2010-07-14 12:18:24 -04:00
Daniel Blankenberg
72c3b8cb89
Enhance VCF to MAF error message when no input file is provided.
2010-07-13 10:44:45 -04:00
James Taylor
bb769367ed
Make "loc files" more flexible by adding "tool data tables". These are
...
configured at the application level. Specific tabular data files are
specified in a application config file and bound to names, the tools
then refer to these names. Thus users can configure where location
files are located without modifying tool configs.
Also:
- Simpler column name configuration
- Columns can be referred to by name in addition to index in all
dynamic option filters
- A data table can merge multiple files
- Design can support other types of data files
2010-07-08 14:36:59 -04:00
Daniel Blankenberg
ff18016e41
Add a VCF to MAF Custom Track converter tool. This tool converts a Variant Call Format (VCF) file into a Multiple Alignment Format (MAF) custom track file suitable for display at genome browsers.
...
This file should be used for display purposes only (e.g as a UCSC Custom Track). Performing an analysis using the output created by this tool as input is not recommended; the source VCF file should be used when performing an analysis.
Unknown nucleotides are represented as '*' as required to allow the display to draw properly; these include e.g. reference bases which appear before a deletion and are not available without querying the original reference sequence.
2010-06-14 15:07:46 -04:00
Daniel Blankenberg
ac86ef683c
Update tool tests for MAF to interval tool
2010-03-09 14:29:17 -05:00
Greg Von Kuster
cf83cecb0b
Better approach to altering initial content of output dataset if necessary. The upload tool will now call the data type's groom_output_dataset() method ( a better name than before_setting_metadata since it is not related to metadata ). This will now also run on the cluster.
2009-12-08 11:46:13 -05:00
John Chilton