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Author SHA1 Message Date
Nate Coraor 3b77d2eaef Fix traceback encountered if you try to access the admin job management interface from a server with job running disabled. 2010-10-21 12:29:58 -04:00
Kanwei Li e9f9451c50 trackster: Don't index bottom level for summary_tree, greatly reducing computation time (>5x speedup) while not sacrificing usability 2010-10-20 18:00:31 -04:00
Nate Coraor 2fb759bd99 Read zipfiles in chunks when uncompressing in the upload tool. And I continue to wish zipfile was a lot more like tarfile... 2010-10-20 17:00:06 -04:00
Jeremy Goecks aa4dc7f746 Do not preserve table borders in Pages. 2010-10-20 16:51:53 -04:00
Jeremy Goecks b43ff3d153 Fix more unicode issues when listing and running workflows. 2010-10-20 16:10:37 -04:00
Jeremy Goecks 760785bd95 Enable display of unicode characters in history and workflow annotations. 2010-10-20 15:52:36 -04:00
Ramkrishna Chakrabarty b8e4e06f11 added more zoom levels for mutation viz tool 2010-10-20 15:34:31 -04:00
Jeremy Goecks f1ca041d6a Update version numbers of Tophat and Cufflinks wrappers to reflect current tool installations on Galaxy main and test instances. 2010-10-20 15:26:58 -04:00
Jeremy Goecks f16b70c403 Add RNA-seq tools -- Tophat + Cufflinks suite -- to main. 2010-10-20 15:14:25 -04:00
Jeremy Goecks dc0075bf9a Fix setting of minimum and maximum values for tracker slider filters. 2010-10-20 00:42:45 -04:00
Kanwei Li 43028dbcc0 trackster: Add proper CIGAR support to BAM display (properly displays matches, deletions, skipped bases, and clipping. Padding and insertions are skipped as of now as there is no good way to insert new space into the view.) 
- Don't re-add new datasets when refreshing after using "Add into current viz" link
- To prevent browser lockup, only display up to 50 lines of features by default (user-editable in future). TODO: add warning message when this occurs
 2010-10-19 18:58:57 -04:00
Ramkrishna Chakrabarty a0103d4796 mutation viz tool help cleanup 2010-10-19 16:40:20 -04:00
Jeremy Goecks 3caf212cab Add dynamic attribute filtering framework for trackster and enable dynamic filtering of VCF quality values and BED score values. Framework enables users to interactively filter a visualized dataset within trackster; for example, a BED file of peaks can be filtering so that only peaks with a score greater than 100 are shown. 
Individual changes include: (a) improvements to datatypes and data providers to support BED score filtering and VCF quality filtering; (b) addition of jQueryUI theme for slider; (c) modifications to trackster to show, update, and apply filters.
 2010-10-19 16:25:51 -04:00
Ramkrishna Chakrabarty 462902909f mutation viz tool test data files 2010-10-19 15:41:22 -04:00
Ramkrishna Chakrabarty 4a0a26eca3 Added tests and more help to mutation visualization tool 2010-10-19 15:38:50 -04:00
Daniel Blankenberg 2684dddbde Add descriptive labels to output dataset names for MACS peakcalling tool. 2010-10-19 13:13:55 -04:00
Ramkrishna Chakrabarty 1d5491c459 Fix for viewing a form definition. 2010-10-18 13:54:38 -04:00
Daniel Blankenberg 94d1cde507 Fix for setting columns in workflow builder for ColumnListParameter. e.g. allows splitting lists of columns by newlines and commas and strips leading 'c's. 2010-10-15 16:09:02 -04:00
Daniel Blankenberg 2469bc7868 Fix for Integer/FloatToolParameter.get_html_field() when 'value' is provided as an integer/float. 
Fixes an issue seen when saving workflows: If an integer or float tool parameter is changed to a value of 0 or 0.0 and saved, the form field would be redisplayed using the default tool value; and not the value that is now saved in the database.
 2010-10-15 14:30:14 -04:00
Kanwei Li 22525a5fe4 trackster: 
- New histogram mode for LineTrack that's used by default.
- Refactored LineTrack drawing code
- Can change draw color of LineTrack
- summary_tree now shows maximum y-axis value
- When editing track config, "Enter" and "Esc" keys submit and cancel the changes, respectively
 2010-10-15 14:24:35 -04:00
Ramkrishna Chakrabarty 5ee541f26d sample tracking functional tests are fixed 2010-10-15 12:49:21 -04:00
Ramkrishna Chakrabarty 83b1fba835 sample tracking 
- create request search+select box bug fixed.
- sample datasets grid operations fixed
 2010-10-15 08:51:30 -04:00
Greg Von Kuster bed3d3987c A bit of code cleanup / optimization in sample tracking. 2010-10-14 11:23:33 -04:00
Ramkrishna Chakrabarty 4631710431 sample_tracking fixes 2010-10-14 00:24:56 -04:00
Kanwei Li 886d6875b7 Show Image type datasets inline in browser 2010-10-13 18:12:31 -04:00
Kanwei Li fbae6b5f6a trackster: Fix ReferenceTrack not drawing, summary_tree display is now histogram and more fine grained. Small overview fix, UI tweaks 2010-10-13 17:59:56 -04:00
Ramkrishna Chakrabarty ed6b6664e3 sample tracking UI fixes 2010-10-13 16:35:39 -04:00
Ramkrishna Chakrabarty 381b72258a sample tracking bug fixes 2010-10-13 16:07:06 -04:00
Kanwei Li c97844d841 No longer try to display Image type (including PDF) datasets within browser. Clicking on eye icon for binary and image types will now invoke save action. 2010-10-13 00:44:09 -04:00
Peter Cock 53a0f91ac7 Support query anchored and HTML output 2010-10-11 12:31:59 +01:00
Peter Cock 581b8cc917 Add -ungapped for blastn and blastx (having trouble with blastp and tblastn, not in tblastx) 2010-10-08 17:18:58 +01:00
Peter Cock df6fa45575 Adding a Python script for converting BLAST XML to 12 column tabular 2010-10-08 16:21:16 +01:00
Peter Cock 53a1469173 Add -word_size as an advanced argument (ideally would be an optional integer with validation) 2010-10-08 12:49:00 +01:00
Peter Cock ea2c417df6 Fixed silly typo 2010-10-06 17:51:45 +01:00
Peter Cock 9269b9d033 Comment out blastn vecscreen as not supported 2010-10-06 17:08:18 +01:00
Peter Cock 9f4289a494 Added support for BLAST+ -max_target_seqs option 2010-10-06 17:07:48 +01:00
Peter Cock 2cf0f766d0 Reduce whitespace in <command> tag (there are OS limits on command line length) 2010-10-06 12:53:38 +01:00
Peter Cock ef49c7ae2f Make BLOSUM62 the default with sensible sorting (tip from Ross Lazarus on mailing list) 2010-10-05 16:52:33 +01:00
Peter Cock 38b83c7d3e Add -matrix option to BLASTP, BLASTX, TBLASTN and TBLASTX (doesn't apply to BLASTN) 2010-10-05 16:48:50 +01:00
Peter Cock 3927b50873 Use dropdown (default) rather than radio for BLAST databases as could be lots of them 2010-10-01 15:57:21 +01:00
Peter Cock 5107e50c46 Updated a caption for consistency, removed an old comment 2010-10-01 15:50:57 +01:00
Peter Cock ef3d585f47 Support -db (database) or -subject (FASTA file) 2010-10-01 14:37:15 +01:00
Peter Cock 1a051f185e Add -strand as adv opt to blastn, blastx and tblastx wrappers 2010-10-01 12:05:41 +01:00
Peter Cock 77fcdf4f4b Don't default to setting seg/dust explicitly (allow BLAST+ to use its own defaults) 2010-10-01 11:47:17 +01:00
Peter Cock a38f4f249b Use a select parameter for picking just column 1 or 2. Less flexible but works better for BLAST output I think 2010-10-01 11:34:07 +01:00
Peter Cock cd0fbe0eb3 Use the data_column type (great except on empty tabular files) 2010-09-30 20:16:30 +01:00
Peter Cock 9bcbbeccff Allow filter to pick ID column 2010-09-30 20:00:15 +01:00
Peter Cock bed7a83e0b Adding blastx and tblastx wrappers, tidying 2010-09-28 16:42:53 +01:00
Peter Cock f9f223cbb3 Adding basic tblastn wrapper 2010-09-28 15:51:39 +01:00
Peter Cock 04a15b7851 Adding simple python script to split a FASTA file into those sequence with/without BLAST hits using tabular output 2010-09-28 14:43:50 +01:00