Kanwei Li
1502eed32f
sam2interval: Add read_name column
2011-08-24 16:43:02 -04:00
Nate Coraor
3cbde2e760
Remove unspecified build validator from aggregate_scores_in_intervals2 tool because it can work with a custom fasta.
2011-08-24 14:38:29 -04:00
Kanwei Li
068ef1df40
Grouping tool: use system numpy if provided, otherwise use bundled numpy egg
2011-08-24 13:58:48 -04:00
Kanwei Li
ad24f8c1dc
Fix sam2interval.py bug due to tab spacing
2011-08-24 13:14:49 -04:00
Daniel Blankenberg
90e695c9aa
Allow FASTQ Groomer tool to work on Color Space files that contain a fake/dummy quality score for the adapter base (e.g. files obtained from the SRA). The Groomer will remove the dummy/fake quality score from the read.
2011-08-22 16:07:23 -04:00
Daniel Blankenberg
8768351b99
Add FIMO tool from MEME suite.
2011-08-22 14:52:11 -04:00
Daniel Blankenberg
aec47aa2a9
pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.
2011-08-22 14:03:57 -04:00
Kanwei Li
a9370f1b72
Spacing fix
2011-08-20 02:56:33 -04:00
Ross Lazarus
d178424fc9
WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported...
2011-08-20 14:27:30 +10:00
Jeremy Goecks
781cef42bd
Add wrapper for Trinity, the de novo RNA-seq transcript assembler ( http://http://trinityrnaseq.sourceforge.net/ ).
2011-08-18 14:20:48 -04:00
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
7169b19f88
Add GTF-guide option to Cufflinks wrapper. Patch from Ilya Chorny.
2011-08-11 10:14:53 -04:00
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
Daniel Blankenberg
591ee9a922
Import patch contributed by Assaf Gordon allowing bwa_wrapper to work directly on fastqillumina formatted files. Closes #635 .
2011-08-08 09:35:48 -04:00
Daniel Blankenberg
33c4c0d4eb
Make setting read groups in BWA off by default.
2011-08-04 13:30:01 -04:00
Ross Lazarus
4720488fa4
Increase lines_diff so sam_merge tests might pass on buildbot
2011-08-04 16:55:13 +10:00
Ross Lazarus
11220e196c
sam_merge.xml tweaks: changed call to MergeSamFiles to use minimal command line flags and finally got LENIENT validation stringency to actually work
2011-08-04 16:50:22 +10:00
Ross Lazarus
5b2e7947ea
Fixed sam_merge.xml to call Picard MergeSamFiles.jar so metadata can be propagated through to the new merged bam from all the individual files - the samtools version of merge would require this to be done separately and passed in with the -h option whereas Picard does it automatically. Added one more test. Interesting that the test for that tool has been failing to correctly pass metadata but passing the buildbot anyway. Thanks to Camille Stephan for pointing out the bug.
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Changes to rgManQQ so the user can obtain a decent pdf image. When millions of points are plotted, these are humongous so GS is called to compress the resulting pdf and they are now of reasonable size. PDF's are now linked from the thumbnails. Some minor fiddling with point size on the Manhatten plots so the intersting ones are a little more obvious.
Minor tweak to twilltestcase.py so composite file components are copied correctly to the directory specified by GALAXY_TEST_SAVE. This makes updating test artefacts much simpler because running tests with GALAXY_TEST_SAVE pointing somewhere will now save every tested output file.
2011-08-04 12:43:30 +10:00
Ross Lazarus
0f1c751800
fixes for rgManQQ plots to create a compressed PDF using GS as the downloadable artifact - much more useful for publication
2011-08-04 10:57:03 +10:00
Jeremy Goecks
75716afeb6
Remove unspecified build validators from Cuffdiff wrapper; fixes #631
2011-08-03 11:39:23 -04:00
Daniel Blankenberg
f9759aac21
Update EuPathDB datasource configuration file. Contributed by Mark Heiges.
2011-08-02 08:55:57 -04:00
Greg Von Kuster
8db279feff
Rewrite Pac Bio assembly_stats tool - it now takes 1 input fasta dataset and produces 1 output tabular dataset. The "wiki" output format has been eliminated, and the dependency on the pbpy module has been eliiminated.
2011-07-28 11:41:01 -04:00
Greg Von Kuster
d8279f0e5c
Add an altered version of Jelle Scholtalbers' enhancement code to support uploding various image data types. I've moved some of the code components around from Jelle's version, and added some fixes. The cod ein the new image_util.py file enables detections of images types without the need to create a new Image() class.
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I've also added baseline support of the HDF5 data type in this change set, but it is currently required to be in the unsniffable_data_types list.
2011-07-27 16:14:15 -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
2f48ff4b28
Cufflinks/compare/diff wrappers: (a) make wrapper versions independent of tool versions; and (b) add comments that indicate tool versions supported by wrappers.
2011-07-21 10:26:41 -04:00
Ross Lazarus
a5e7d020a6
Minor tweak to the x axis sorting of Manhattan plots to fix the fact that in R, unique() returns an alphabetically sorted list - need to use sort on the result to get correct lexicographic (10 comes after 9 eg) on the X axis...
2011-07-20 13:34:27 +10:00
Kanwei Li
6f2ce426d9
Merged in semenko/galaxy-central-replace-bitbucket (pull request #2 ) for wiki links
2011-07-19 22:18:40 -04:00
Ross Lazarus
7d2dd59186
Fixes to rgManQQ.py to handle chromosome oddities like 'chr1' and X.
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Also cleaned up redundant file recreation - the code passes column numbers to R so the raw data can be read as supplied by Galaxy
Thanks to Alison Harrill for exposing some more input edge cases...
2011-07-20 12:17:43 +10:00
Nick Semenkovich
403f2c73a3
Update links to reflect Galaxy Wiki moving away from Bitbucket.
2011-07-18 18:10:55 -05:00
Guruprasad Anada
c3fc61d296
Fixed a bug in PCA tool - standard deviation & prop variance values are now sorted by PC order.
2011-07-15 10:33:02 -04:00
Kanwei Li
286c8f2af6
Improve BLAST parser tool error handling, and improve elementtree import as well.
2011-07-12 18:14:56 -04:00
Kanwei Li
7282f0ac10
Rename version_string -> version_command, update wrappers
2011-07-12 17:04:16 -04:00
Peter Cock
d3157a5ed7
Support new tool version tag in NCBI BLAST+ wrappers
2011-07-07 11:19:33 +01:00
Daniel Blankenberg
d09305f56b
Update annotation profiler tool sample configuration file.
2011-07-07 12:13:49 -04:00
Kanwei Li
5c0323d4d8
Add tool version-string support to tool wrappers. Use the <version_string> tag to denote the command to run for the tool version, such as: tophat --version (see tophat wrapper change for example)
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The tool version string will currently be appended to the Info string in the history dataset and you will be able to see it in the history pane, although this might be added to the database as well in the future.
2011-07-06 22:37:51 -04:00
Ross Lazarus
903d828618
More comprehensive error detection for weblogo installation or execution errors
2011-07-07 10:04:20 +10:00
Ross Lazarus
a27b048a64
committing backout from 5765 which included reversions from a broken galaxy-central repository
2011-07-06 09:45:41 +10:00
Ross Lazarus
d53c3e984f
Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository
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This is a backout of commit 5765
2011-07-06 09:44:56 +10:00
Ross Lazarus
01cf808679
Added new test and optional x axis unit alternatives (bits/probability/kcal etc) to weblogo as suggested by Assaf Gordon
2011-07-05 16:46:21 +10:00
Ross Lazarus
86b55bb0c0
branch merge
2011-07-05 12:40:43 +10:00
Guruprasad Anada
5c978b62bd
Rounded the outputs of regression to 10 significant digits.
2011-06-27 15:44:59 -04:00
Kelly Vincent
b2b107724b
Add missed dbkey setting to Tophat color-space wrapper
2011-06-27 11:20:04 -04:00
Kelly Vincent
20f77b2a71
Added color-space Tophat wrapper
2011-06-24 16:55:43 -04:00
Jeremy Goecks
1317c5da1f
Better handling of Cuffdiff outputs when set_metadata_externally=True
2011-06-22 08:36:48 -04:00
Richard Burhans
a3d79b20ed
updated error handling for genome diversity select snps tool
2011-06-17 12:16:53 -04:00
Jeremy Goecks
5355a95ef3
Trackster improvements: (1) add trackster_conf tag to tool definition; for now, tag indicates that tool is compatible with trackster, but will have configuration information in the future; (2) use trackster_conf tag to indicate that Cufflinks, gops intersect, and gops subtract are compatible with Trackster; and (3) remove .track_type attribute and use of it and use instanceof operator instead.
2011-06-16 10:22:31 -04:00
Richard Burhans
423554ee36
tweaks to get genome diversity tools to pass their functional tests
2011-06-15 17:10:51 -04:00
Richard Burhans
0dfb7336c4
updates to genome diversity tools
2011-06-15 15:51:05 -04:00
Jeremy Goecks
a4b56c0b74
Improve filtering tool's stdout reporting of lines filtered; fixes #536
2011-06-15 13:22:18 -04:00
Kanwei Li