Dannon Baker
03351d2a9f
Apply black to tools as well
2022-02-03 09:12:13 -05:00
Michael R. Crusoe
7819fdc7a6
tighten type ignores
2021-11-23 13:12:07 +01:00
John Chilton
2a0474730b
Rev mypy.
2021-04-23 14:49:53 -04:00
Nicola Soranzo
d26b3d9848
Fix all E203, E741 and W504 flake8 errors
2021-01-18 10:35:41 +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
7c1cacebbd
Consistent "import" of maketrans
...
Trying first with the most recent version is considered more Pythonic,
I think.
2020-02-11 03:46:25 +00:00
Nicola Soranzo
85f7f91206
Fix script shebangs
...
Improve tools.
2019-10-26 20:20:01 +01:00
mvdbeek
77b43946f6
Fix solid2fastq tests
2018-09-05 14:22:01 +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
ed4132d9c0
Python3: Use open() instead of file()
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
peterjc
fce2184e5b
Make tool version explicit (Job runner would assume 1.0.0)
2015-03-09 15:21:48 +00:00
Nicola Soranzo
f73d5fba6c
Fix old wiki links.
2014-04-10 20:00:45 +02:00
Dave Bouvier
95a66294d6
Fixed error in solid2fasta.xml preventing help text from displaying.
2012-09-04 10:15:18 -04:00
Nick Semenkovich
403f2c73a3
Update links to reflect Galaxy Wiki moving away from Bitbucket.
2011-07-18 18:10:55 -05:00
Anton Nekrutenko
81cbebafd4
solid2fastq now correctly errors out for out-of-sync solid files. Adderesses user reported bug from yjx@rice.edu
2011-06-08 16:25:15 -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
Anton Nekrutenko
04ed0933cf
Updated output format for solid2fastq converter
2010-04-07 08:44:57 -04:00
Kanwei Li
0952b28502
Sync hashbangs
2010-04-01 20:36:31 -04:00
Greg Von Kuster
927cfe685c
Fixed my previous fix for copying history items to a library, which really didn't fix anything.  Fixed the functional tests for lav_to_bed, split_paired_reads, and solid2fastq by adding the 2nd output dataset to the test for each tool.  Renamed the test files for the tools to have the Galaxy supported file extension.
2010-01-14 09:44:58 -05:00
Anton Nekrutenko
9d6a9ee9b2
Small fixes to solid2fastq
2010-01-06 11:56:55 -05:00
Anton Nekrutenko
73db93f7bb
Smart converter for SOLiD, which takes care of F3-R3 pairing problem. Requires python2.5
2010-01-05 14:33:39 -05:00
Kelly Vincent
d8c406cc14
Updated solid_to_fastq so that -1 qualities are converted to 1 before conversion to FASTQ.
2009-10-21 16:04:24 -04:00
Kelly Vincent
6dc8d3b3c4
Modified Solid_to_Fastq's underlying perl script so that it would not produce the None file, and also uncommented tests and updated example
2009-10-13 16:49:38 -04:00
Kelly Vincent
ffcb0aac03
Changed FASTQ Groomer's handling of Sanger data to output all lines even if only first n are validated
2009-10-12 14:04:28 -04:00
Anton Nekrutenko
809f774f36
ngs updates
2009-10-07 11:18:14 -04:00
Kelly Vincent
91de8aceb4
Added FASTQ \"Groomer\" tool to converters section. Relies on new datatype (fastq) which will be added later.
2009-10-06 21:25:01 -04:00
Kelly Vincent
1b0c05e257
Modified solid to fastq converter tool to specify path to perl script that does conversion
2009-09-24 14:09:17 -04:00
Kelly Vincent
bbfde2c0cd
Added header removal option to BWA wrapper tool, and cleaned up its test files. Also added the bwa_solid2fastq_modified.pl script to the next gen conversion directory for the solid-to-fastq tool.
2009-09-18 12:11:43 -04:00
Kelly Vincent
45201c6054
Updated BWA wrapper tool: replaced threads option to hard-coded value, changed output and test file output datatype to sam, changed test file names to standard, better cleanup of temp files, added dbkey parameter and exec_before_job method to set it. Also changed name of a FASTQ Conversions tool test file
2009-09-16 11:14:39 -04:00
Kelly Vincent
f5d67cda72
Renamed test files and fixed output datatype problem with solid-to-fastq tool
2009-08-04 16:32:57 -04:00
Kelly Vincent
57f0f10d38
Commented out failing test in solid_to_fastq and added test files that fastq_conversions relies on
2009-08-03 16:58:22 -04:00
Kelly Vincent
5d4b1151d0
Added solid_to_fastq and fastq_conversions converters to Convert Formats section
2009-07-31 11:48:37 -04:00
Dannon Baker