 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 |
|