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152 Commits
Author SHA1 Message Date
Dannon Baker 03351d2a9f Apply black to tools as well 2022-02-03 09:12:13 -05:00
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
John Chilton 2a0474730b Rev mypy. 2021-04-23 14:49:53 -04:00
Nicola Soranzo 452aba9ee3 Fix remaining issues reported by bugbear; add it to flake8 reqs 2021-01-16 05:58:15 +00:00
Matthias Bernt 62be881d92 fix shrimp_color_wrapper 2020-04-27 19:05:01 +02:00
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 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
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 d1bc98dfcb Python3: fix remaining print statements 
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
 2017-10-12 18:34:29 +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 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
Nicola Soranzo 39da6c3278 Fix the remaining 2180 flake8 errors in tools/ . 2016-02-10 18:46:03 +00:00
Dave Bouvier a3018feb02 Migrate 22 tools from the distribution to the tool shed. 2014-05-19 13:01:46 -04:00
Dave Bouvier 5f485f05b3 Remove tool that was migrated to the tool shed in 10719:c2f06b5cfba1. Remove test data that belonged to tools that were removed in 12288:401ee23dcf2f. 2014-02-17 13:05:00 -05:00
John Chilton cfb194f0a0 Enhance megablast to utilize GALAXY_SLOTS configuration when available. 2013-11-05 13:46:06 -06:00
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
Anton Nekrutenko 8cda02d849 Fixed number of threads 2012-04-26 16:49:38 +02:00
Anton Nekrutenko a2eb104b31 Modified metagenomic mapper to use BLAST+ blastn in megablast mode 2012-04-26 16:44:26 +02:00
Daniel Blankenberg 023c4db69e Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools. 2011-11-29 17:30:14 -05:00
Kanwei Li 286c8f2af6 Improve BLAST parser tool error handling, and improve elementtree import as well. 2011-07-12 18:14:56 -04:00
Nate Coraor b77ec95d0b Fix for either a bug or undocumented feature in ElementTree that broke megablast and blast+ XML parsing in Python 2.7. 2011-06-09 11:22:23 -04:00
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
Kelly Vincent 7d0ff14df9 Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters. 2010-11-08 00:10:13 -05:00
Nate Coraor e05f11bc73 Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'. 2010-10-07 16:23:57 -04:00
Nate Coraor 7c71894533 Remove obsolete binseq.zip and txtseq.zip formats, and allow for uploading single files in a zip archive. Adapted from a patch from Pablo Cingolani. 2010-06-23 16:48:13 -04:00
Kelly Vincent eeca0c723a Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output 2010-04-12 15:56:13 -04:00
Kanwei Li 0952b28502 Sync hashbangs 2010-04-01 20:36:31 -04:00
Kelly Vincent 38ad670389 Updated several NGS tools to better handle stderr (allow for extremely large stderr output) 2010-03-30 16:33:19 -04:00
Nate Coraor 0bfa58679b Fix locations of cached data for tests 2010-02-25 12:27:07 -05:00
Daniel Blankenberg 8082c6f36f Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid. 
Tools include:
	FASTQ Groomer convert between various FASTQ quality formats
	Combine FASTA and QUAL into FASTQ
	FASTQ joiner on paired end reads
	FASTQ splitter on joined paired end reads
	FASTQ to FASTA converter
	FASTQ Summary Statistics by column
	Filter FASTQ reads by quality score and length
	FASTQ Trimmer by column
	Manipulate FASTQ reads on various attributes
	Boxplot of quality statistics (Generic, with outliers)
 2010-02-23 16:48:07 -05:00
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
Guruprasad Anada fb9147e83d Fixed functional tests for short_reads_figure_score tool. 2010-01-08 11:28:37 -05:00
Nate Coraor 49a0fcc92f fix for parsing blastdb.loc for the megablast wrapper tool 2009-12-15 19:18:22 -05:00
Greg Von Kuster aa36d79d30 Update the output datasets for functional test for the quality_score_distribution tool due to a new version of R - update tool version as well. 2009-12-10 10:56:01 -05:00
Kelly Vincent ebc67a6bc7 Updated megablast_wrapper tool to allow for date to be included with database name and displayed (so user knows how current it is) 2009-12-09 18:50:12 -05:00
Nate Coraor 56032de2bd Upgrade to Cheetah 2.2.2 2009-11-10 13:47:34 -05:00
Kelly Vincent 03cb53ead3 Fixed megablast_wrapper test to use phiX database and modified parameter passing to use named parameters 2009-11-10 13:06:20 -05:00
Anton Nekrutenko 854fb020b8 Modified test data and tool conf for fastq stats 2009-10-08 14:50:28 -04:00
Anton Nekrutenko 809f774f36 ngs updates 2009-10-07 11:18:14 -04:00
Kanwei Li 3531212ff6 typo fixes for tools in folders A-M 2009-09-27 23:11:43 -04:00
Anton Nekrutenko 13c7b84abb Second pass of help and interface updates. Not done yet... 2009-09-22 08:59:36 -04:00
Anton Nekrutenko 2105021def small tweaks 2009-09-18 11:11:41 -04:00
Anton Nekrutenko c4b8764d6f Modification for input datatype in the splitter:w 2009-09-15 10:30:54 -04:00
Anton Nekrutenko 28ccd18f7d Modifications for fastq splitted help 2009-09-14 15:27:55 -04:00
Anton Nekrutenko bf9666bf21 Fixed a stupid and truly horrible paired end splitter bug 2009-08-20 17:33:39 -04:00