 Daniel Blankenberg
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4685ec3f8a
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Enhance Bowtie wrapper to accept non-sanger variant FASTQ files.
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2011-03-02 11:40:58 -05:00 |
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Daniel Blankenberg
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2935741194
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Allow FromParamToolOutputActionOption and ParamValueToolOutputActionOptionFilter to access attributes of parameter values.
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2011-03-02 11:34:36 -05:00 |
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Daniel Blankenberg
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ad3f55b5b0
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Allow DataToolParameter to be filtered on attributes other than dbkey.
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2011-03-02 11:34:03 -05:00 |
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Greg Von Kuster
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4bdc069c4d
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Clarify what's being searched in the tool shed.
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2011-03-02 09:59:24 -05:00 |
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Ramkrishna Chakrabarty
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bdb4ec4505
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Fix for vcf_extract tool test
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2011-03-02 09:40:10 -05:00 |
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Dannon Baker
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a9548d1a07
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Remove ftype from mosaik/freebayes test outputs.
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2011-03-02 08:38:19 -05:00 |
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Nate Coraor
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0411837b7b
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Drop the ftype attribute from tophat test outputs
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2011-03-02 08:28:30 -05:00 |
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Kanwei Li
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fac370ce4e
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trackster: Difference view setting for ReadTracks: only see sequence on reads if they don't match reference. Align sequence with positional ticks.
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2011-03-01 16:39:46 -05:00 |
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Nate Coraor
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3fc4c7c4f8
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Enable the ftype attribute for test outputs, fixes the sam-to-bam test.
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2011-03-01 15:46:35 -05:00 |
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Nate Coraor
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cb9bbd0e0b
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Update bwa_color_wrapper cached indices name to match the key used in the test data repository
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2011-03-01 15:21:25 -05:00 |
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Daniel Blankenberg
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5bff82eb46
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Have YeastMine datasource tool point to the production server location and add configuration to tool_conf.xml.main.
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2011-03-01 13:00:27 -05:00 |
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Daniel Blankenberg
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7fb03e7768
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Remove unused parameters from TopHat and Cufflinks tool tests.
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2011-02-28 15:17:35 -05:00 |
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Ramkrishna Chakrabarty
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58284e4848
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Adding tests for vcf extract and filter tools
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2011-02-28 15:03:45 -05:00 |
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Dannon Baker
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48b65e9b17
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mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag.
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2011-02-28 14:32:36 -05:00 |
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Guruprasad Anada
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4a94876feb
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Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool.
Also, fixed a bug in microsatellite birth/death tool - cases where microsatellite boundaries aren't defined are skipped.
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2011-02-28 14:04:53 -05:00 |
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Daniel Blankenberg
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4eb1b0a79f
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Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
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2011-02-28 12:16:28 -05:00 |
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Jeremy Goecks
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09cd28148f
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Fix bad value in cufflinks functional test.
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2011-02-28 09:59:30 -05:00 |
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Nate Coraor
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154b8c61ce
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Bugfix for the last commit when running functional tests with sqlite.
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2011-02-28 09:52:17 -05:00 |
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Nate Coraor
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b4506597e6
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Require ctypes egg before pysam on Python 2.4
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2011-02-28 09:35:36 -05:00 |
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Nate Coraor
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e8a11ffd6c
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Add ccat_configurations.loc to buildbot_setup.sh
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2011-02-28 08:33:48 -05:00 |
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Nate Coraor
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8e995a23be
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Increase the SQLAlchemy SuquePool limits for functional tests.
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2011-02-28 07:58:52 -05:00 |
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Jeremy Goecks
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c5ac00b7db
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Suppress most logging for cufflinks and cuffdiff as the logging can generate output that is incompatible with UTF-8 format used by database.
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2011-02-27 14:48:23 -05:00 |
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Nate Coraor
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e5fbc191c2
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Add mosaik index location file to buildbot setup.
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2011-02-26 13:12:44 -05:00 |
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Dannon Baker
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4d499816e3
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Basic Freebayes test added.
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2011-02-26 10:53:50 -05:00 |
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Dannon Baker
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11f15b123b
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Freebayes and Mosaik updates
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2011-02-25 17:53:58 -05:00 |
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Ramkrishna Chakrabarty
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5ddadf7921
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Fixed adding an external service to a request type in edit_request_type
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2011-02-25 16:25:54 -05:00 |
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Ramkrishna Chakrabarty
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3a88ba4cdb
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Bug fix: do not show sample field widgets in the view request page
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2011-02-25 16:12:17 -05:00 |
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Ramkrishna Chakrabarty
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974efda97a
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First pass of extract & filter VCF tools.
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2011-02-25 15:58:13 -05:00 |
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Kanwei Li
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43db543f1f
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Update test-data files for meme 4.6.0
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2011-02-25 14:58:35 -05:00 |
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Kanwei Li
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096e95ff41
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Typos
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2011-02-25 13:35:27 -05:00 |
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Kanwei Li
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ac2d5a8f69
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Only lowercase columns if starting with "c".. fixes issue where "None" was lowercased to "none". Fixes subtract_query tests
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2011-02-24 19:07:41 -05:00 |
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Dannon Baker
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1dc6f33ca7
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workflows: Will never collapse steps containing workflow parameters by default now.
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2011-02-24 18:21:46 -05:00 |
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Dannon Baker
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d7cd1c5b2a
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workflows: Fix parameter replacement in long inputs where the parameter isn't the whole value.
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2011-02-24 18:08:15 -05:00 |
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Kanwei Li
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2d0ade7288
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Update jQuery to 1.5.1, and also jquery.form as old one was incompatible with 1.5
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2011-02-24 17:23:16 -05:00 |
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Kanwei Li
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29f602f1fd
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Updated bigBed test file
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2011-02-24 16:19:03 -05:00 |
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Jeremy Goecks
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39bfd3c89d
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Add options to Tophat wrapper to support v1.2.0 functionality: (a) allow indel search; (b) max insertion and max deletion lengths; and (c) library type. Update functional tests to tests new options. Also update function that checks from_work_dir output attribute to use real path to prevent mishandling of symbolic links.
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2011-02-24 15:24:52 -05:00 |
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Kanwei Li
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036082793b
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Fix bed_to_bigBed test
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2011-02-24 15:23:21 -05:00 |
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Kanwei Li
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8d203efef1
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Fix BLAST+ test
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2011-02-24 15:07:46 -05:00 |
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Kanwei Li
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dfed222fcb
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Fix debugging output on BLASTX+ failure
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2011-02-24 12:27:37 -05:00 |
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Ramkrishna Chakrabarty
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47a61afa18
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Adding ftype attribute to vcf tool tests
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2011-02-24 12:16:33 -05:00 |
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Jeremy Goecks
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3b3cf4c995
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Update functional test outputs for v1.2.0 of Tophat.
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2011-02-24 09:17:50 -05:00 |
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Nate Coraor
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e1ea63eb9a
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When comparing bam files in the test framework, convert them to sam for comparison.
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2011-02-23 14:53:54 -05:00 |
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Dannon Baker
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668d03ba7d
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Initial commit of Mosaik and Freebayes.
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2011-02-23 14:01:58 -05:00 |
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Nate Coraor
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7ef6723533
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Update bwa_wrapper to use the test data repository. bwa_color_wrapper will need to be done once the test data repository is updated to contain the data it uses.
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2011-02-23 13:54:06 -05:00 |
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Ramkrishna Chakrabarty
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0e7e0241fb
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Bug fix: checkbox values were not getting saved for samples in the sample grid. Issue #476
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2011-02-23 11:56:16 -05:00 |
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Jeremy Goecks
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85a065cd5b
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Enhance GFF reader to handle headers and comments.
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2011-02-23 10:40:30 -05:00 |
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Kanwei Li
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fb1a345ebe
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Refactor javascript in tool_form.mako; fix indentation for repeat groups
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2011-02-22 18:49:57 -05:00 |
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Jeremy Goecks
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ef28a2cb36
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Set output dataset type for 'Extract GFF features' tool to be input dataset type.
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2011-02-22 18:41:15 -05:00 |
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Kanwei Li
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ab44dae254
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Remove overflow from help text in tool forms, for IE
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2011-02-22 18:10:52 -05:00 |
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Kanwei Li
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d224c1056c
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Fix IE error when clicking on links in tool pane. Small refactoring as well
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2011-02-22 17:24:10 -05:00 |
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