John Chilton
77b167bbd1
Comment out broken liftOver tests.
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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.
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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.
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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.
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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"
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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.'
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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.
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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
Ramkrishna Chakrabarty
468a631370
Applied patch provided by Brad Chapman in the liftOver tool to support BED files that contain track or browser lines. Resolves bitbucket issue 201.
2009-11-12 13:20:19 -05:00
Kanwei Li
3531212ff6
typo fixes for tools in folders A-M
2009-09-27 23:11:43 -04:00
Guruprasad Anada
d72d1a7205
Change dbkey of unmapped liftover dataset to the input dataset's dbkey.
2009-08-21 11:40:51 -04:00
Guruprasad Anada
0e29e97366
Committing changes to 'extract genomic dna' tool - twobit file will be opened only once per job. (Courtesy: Gordon).
2009-07-20 16:57:55 -04:00
Guruprasad Anada
15652612b7
A bug fix for extract genomic dna to handle invalid chromosomes correctly.
2009-07-07 12:06:35 -04:00
Guruprasad Anada
018537baf6
Extract genomic DNA tool now uses only alignseq.loc to access sequence files. The twobit.loc file will henceforth be unnecessary, and all sequences from it should be moved to alignseq.loc.
2009-06-25 15:29:24 -04:00
Guruprasad Anada
167ce59b29
Bug fixes for histogram liftover and grouping tools.
2009-05-29 11:07:18 -04:00
Guruprasad Anada
d0c13d7ec4
Added a new option to specify minimum match value in the liftOver tool.
2009-04-03 13:25:01 -04:00
Guruprasad Anada
d6d59f7431
Added Validator to a bunch of tools..
2008-10-17 13:02:26 -04:00
Daniel Blankenberg
61ca17eade
Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.
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Several tools have been updated to take advantage of this, eliminating their need for code_files.
2008-09-30 16:17:12 -04:00
Greg Von Kuster
4f56b82e17
Fix for dataset_metadata_in_file validator: all locally cached data files that are columnar must have columns separated by tabs characters, not white space. I've eliminated the 'split' param from the validator as it was causing problems. Extract genomic DNA tool should now finally work correctly.
2008-08-22 11:22:44 -04:00
Greg Von Kuster
5618fa0a2e
(no commit message)
2008-08-21 16:49:16 -04:00
Greg Von Kuster
57ac81b508
Reverting extract_genomic_dna and blat_wrapper tools to rev 1472.
2008-08-21 08:54:51 -04:00
Greg Von Kuster
052444000c
Unbreaking 2 tools that I just broke.
2008-08-19 13:35:44 -04:00
Greg Von Kuster
374b08b963
Some tool fixes:
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1) fix for interval_maf_to_merged_fasta when strand column not included in input metadata
2) Tools using alignseq.loc now split on TAB rather than wihite space
2008-08-19 10:44:08 -04:00
Greg Von Kuster
02f2ff3c85
Fix for Extract Genomic DNA when input file metadata missing strand column value.
2008-08-12 09:18:47 -04:00
Greg Von Kuster
5dd014a91e
Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.
2008-07-23 15:27:39 -04:00
Greg Von Kuster
f931001667
Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.
2008-06-30 18:02:53 +00:00
John Chilton