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v18.05
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175 Commits
Author SHA1 Message Date
Nicola Soranzo 2515267ca5 Add version attribute to tool requirements 
instead of relying on `lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml` .
Follow-up on https://github.com/galaxyproject/galaxy/pull/5544 .

See https://github.com/galaxyproject/galaxy/pull/5544/files#r183909746 for
an explanation why that's preferrable for future-proof reproducibility.

Also, small fixes to `tools/evolution/codingSnps.xml` .
 2018-04-25 15:50:35 +01:00
John Chilton 7712f69b69 Rev tool versions for tools with updated ucsc tool requirements. 2018-04-24 14:40:28 -04:00
Nate Coraor 4b09027ebb Update all tools/converters using UCSC binaries to depend only on the 
binary they are using.
 2018-02-15 10:54:04 -05:00
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
mvdbeek 3dbdf7d474 Make liftover tool use data table 2017-09-19 16:09:36 +02:00
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 69cda48690 Remove remaining references to galaxy.eggs . flake8 some files in tools/ . 2015-10-26 19:29:13 +00:00
yhoogstrate 6a38e0bda7 Update liftOver_wrapper.xml 
version++
 2015-08-12 10:57:42 +02:00
youri 83bc5b74ff liftOver.loc was not accessible from local data 2015-08-11 10:58:06 +02:00
y.hoogstrate@erasmusmc.nl 6ce94ce7e6 Fixed comments 2015-07-30 13:12:51 +02:00
y.hoogstrate@erasmusmc.nl 91a29d8a6a extract_genomic_dna support for 2bit files from Local data 2015-07-30 12:06:07 +02:00
Nicola Soranzo 22d4a1d8c3 dos2unix of tools/ directory. Some whitespace and PEP-8 fixes. 2015-05-15 12:40:52 +01:00
John Chilton 77b167bbd1 Comment out broken liftOver tests. 
liftOver loc file handling is problematic (https://trello.com/c/A6I6zQvF). If it weren't this wouldn't be a problem. I could fix the API functional test framework to mimic the older form driven approach but it would take a week and would be rendered moot by fixing liftOver. Unfortunately, fixing liftOver would likely break a lot of existing workflows and tool reruns so I am not fixing that either.

Only option left, admittedly a crappy one, is to comment out the tests.
 2015-02-23 23:09:19 -05:00
Daniel Blankenberg 8ccf8287b4 Quote commandline arguments for extract genomic DNA tool. 2014-09-02 13:15:17 -04:00
Nate Coraor 9c64fc123e Remove broken and/or obsolete tools. 2014-01-27 13:58:31 -05:00
John Chilton 32b07c04f3 Rev slightly the tool version of extract_genomic_dna.xml since output is slightly different. 
Update tool help to reflect new output format.
 2013-10-25 00:06:14 -04:00
John Chilton 54a3dba91e Update hg17 test case for extract_genomic_dna.xml tor reflect recent changes. 
Cannot delete or modify previous output file - it is used as input for another tool. Use assertion testing to weaken test case. As this tool is migrated to the tool shed the hg17 test cases should probably be eliminated completely.
 2013-10-25 00:03:57 -04:00
Bjoern Gruening f444f30235 bugfix and one test fix 2013-10-24 18:13:18 +02:00
Bjoern Gruening 11b74295d2 Add the value (nameCol) in a given BED file to the FASTA header. 2013-10-18 18:31:44 +02:00
John Chilton 0d3922850e Add ucsc_tools requirement for extract_genomic_dna.xml tool. 2013-09-03 12:32:02 -05:00
Dave Clements f706f34948 Replaced "query" with "dataset" in a number of tool definition XML files. 
I got tired of coming across "query" when doing workshops.
 2013-01-14 16:13:54 -08:00
Jeremy Goecks 2ebe0eb774 Clean up temp files. 2012-03-09 16:11:21 -05:00
Ross Lazarus d5bd7132c1 remove validator from input genome - as Jeremy pointed out it will prevent the use of an unspecified build local genome. 2012-02-25 08:48:03 +11:00
Ross Lazarus 4c23088864 Add a validator type="unspecified_build" 
to extract genomic dna tool
 2012-02-24 18:27:34 +11:00
Jeremy Goecks 08cfd112cd (1) GFF parsing improvements; and (2) output improvements for extract genomic dna tool. 2011-08-14 19:49:26 -04:00
Peter Cock 29bc117ac1 Add missing requirement and fix incorrect help text in extract sequence tool 2011-08-12 10:33:26 +01:00
Jeremy Goecks 92e2f4f48b Remove unspecified build validator from extract_genomic_dna tool because it can work with a custom fasta. 2011-08-11 09:53:14 -04:00
Guruprasad Anada feb0b91aba Added additional options to the liftOver tool. It now supports GFF and GTF formats and allows multiple output regions and related options. 2011-07-26 16:14:31 -04:00
Jeremy Goecks 108e3f8494 Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior. 2011-02-16 21:46:23 -05:00
Jeremy Goecks ae6cb82e01 Bug fix: do not fix strand in extract_genomic_dna tool. 2011-02-16 12:56:18 -05:00
Jeremy Goecks 98a3a358e0 Fix bug in extract_genomic_dna.py so that comment lines are correctly handled. 2011-02-14 13:21:04 -05:00
Jeremy Goecks 23a8b191a7 Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality. 2011-02-10 17:19:40 -05:00
Jeremy Goecks 9fb9279584 Move gff_util.py from galaxy/tools/util to galaxy/datatypes/util because gff_utils are now used by the framework as well as tools. 2010-11-14 11:29:44 -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
Jeremy Goecks e3dcfc89a7 Fix filenames problem in 'extract genomic dna' GFF functional tests that was introduced in 4200:291183d3896b . 2010-09-01 09:10:58 -04:00
Jeremy Goecks bcc1e7b76c Add tool 'gff_filter_by_feature_count', create 'GFF' subheading under Tool Menu's Filter category for GFF filtering tools, and rename 'gff_filtering' tool 'gff_filter_by_attribute.' 
gff_filter_by_feature_count tool filters a GFF file using conditions based on transcripts' features counts; for example, it is possible to filter for transcripts that have a minimum number of exons or transcripts that have 3' UTRs.

Added GFF subheading to Tool Menu under Filtering and placed all GFF filtering tools under this heading.
 2010-08-26 12:00:41 -04:00
Daniel Blankenberg f97a380a56 Add ToolOutputActions to set dbkeys for LiftOver tool and both Bowtie wrappers; remove no longer needed code files. 2010-08-09 21:06:18 -04:00
Jeremy Goecks e96e38e527 Fix bug so that fasta identifier produced by 'extract genomic dna' tool for GFF files is consistent with GFF coordinates. 2010-07-15 17:03:14 -04:00
Jeremy Goecks eba71eb234 Enable 'extract genomic DNA' tool to accept and produce GFF files and added functional tests for this feature. 2010-07-08 15:43:22 -04:00
Kelly Vincent 44fb42f6a0 Fix try-except-finally bug to be compatible with Python 2.4 in several tools and twilltestcase.py. Updated liftOver test to replace hard-coded (incorrect) path and modified code file to allow for new path. Improved bowtie error handling. 2010-03-10 11:51:00 -05:00
Nate Coraor 0bfa58679b Fix locations of cached data for tests 2010-02-25 12:27:07 -05:00
Guruprasad Anada 22b3dfa1c2 Added functional tests for a couple of my tools with multiple outputs/pdf outputs. 2010-02-03 13:53:16 -05:00
Daniel Blankenberg 4d7be79a2b Have Extract Genomic DNA tool copy metadata from input file. 
This will allow the tool to keep column assignments when outputing interval format.
 2009-11-16 10:57:31 -05:00
Greg Von Kuster 527e1258f1 Change the version of the liftOver tool due to the application of Brad Chapman's patch in change set 3021. 2009-11-13 14:20:03 -05:00