Nate Coraor
3fc4c7c4f8
Enable the ftype attribute for test outputs, fixes the sam-to-bam test.
2011-03-01 15:46:35 -05:00
Daniel Blankenberg
4eb1b0a79f
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/.
2011-02-28 12:16:28 -05:00
Daniel Blankenberg
0ee635749d
Change output format of samtools flagstat from 'text' to 'txt'.
2011-01-26 15:45:27 -05:00
Kelly Vincent
8c13d8e6e8
Corrected output labels to be in line with other tools for NGS tools: sam_to_bam, sam_merge, sam_pileup, bam_to_sam, PerM, bowtie_color_wrapper, bowtie_wrapper, bwa_wrapper, lastz_paired_reads_wrapper, lastz_wrapper, srma_wrapper
2011-01-12 13:31:04 -05:00
Daniel Blankenberg
2a510df4aa
Add samtools flagstat tool.
2010-12-15 23:39:16 -05:00
Kanwei Li
2d0b8eb830
Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141
2010-12-14 14:22:13 -05:00
Kelly Vincent
f61d147034
Added --max and --un file output options to Bowtie and modified tests to test for them.
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Made Bowtie test files longer (more than one test read).
Added explanation of canonical and full reference genome variants to BWA and Bowtie.
Added informative labels to output files for NGS tools.
2010-12-01 10:54:35 -05:00
Kelly Vincent
d149382f05
Added version info to stdout for NGS tools
2010-11-24 12:35:49 -05:00
Kanwei Li
ba597f99d7
Refactor sam_bitwise_flag_filter tool, simplifying it and making it faster, especially when there are multiple flag criteria
2010-11-13 14:37:26 -05:00
Dannon Baker
988d94f2d4
Minimally functional splitting.
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Disabled by default, not advisable to enable on a production server (or main!) until scheduling issues are looked at and performance analysis has been done.
Tested 'basic' splitting with many basic tools (bowtie, bwa, filter sam, others). This style of splitting should work for most 'embarassingly parallel' one input, one output tools (no dependence between parallel tasks).
2010-11-10 12:06:05 -05:00
Kelly Vincent
ab1e01e928
Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers
2010-11-08 15:00:54 -05:00
Nate Coraor
ea320b845b
Remove imports of the sets module, set has been a standard type since 2.4. There are more in tools, but they check for the existence of set() first, so will not raise a warning.
2010-09-27 21:35:03 -04:00
James Taylor
e2ae2c4a75
Requirements tags for some samtools tools
2010-09-26 18:06:01 -04:00
Kelly Vincent
33bd292e41
Added BAM-to-SAM tool
2010-09-01 09:44:12 -04:00
Kelly Vincent
5c546a21b3
Updating sam_indel_filter tool; adding NGS: Indel Analysis section; adding indel_analysis, indel_table, and indel_sam2interval tools
2010-07-14 01:09:52 -04:00
Kelly Vincent
862531e04e
Changed the way sam_indel_filter expects quality score cutoffs and fixed bug so it checks qualities for correct bases in all cases
2010-06-24 13:43:38 -04:00
Kelly Vincent
7373e78cd4
Fixed handling of alignments with CIGAR strings with multiple indels for SAM indel filter, plus updated test files
2010-06-10 13:19:43 -04:00
Kelly Vincent
78b17cbb9c
Adding SAM indel filter tool with test files
2010-06-07 15:23:32 -04:00
Kelly Vincent
139c2cf667
Change the way size of output file determined in Bowtie and SAM-to_BAM to deal with memory limitation.
2010-04-30 15:27:41 -04:00
Anton Nekrutenko
008cc9a012
changes to help text
2010-04-15 11:10:57 -04:00
Anton Nekrutenko
254ad33d95
Fixed indel calling in pileup wrapper. TO DO: Write a separate wrapper for indels only.
2010-04-14 13:52:35 -04:00
Kelly Vincent
eeca0c723a
Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output
2010-04-12 15:56:13 -04:00
Anton Nekrutenko
04ed0933cf
Updated output format for solid2fastq converter
2010-04-07 08:44:57 -04:00
Kanwei Li
0952b28502
Sync hashbangs
2010-04-01 20:36:31 -04:00
Kelly Vincent
38ad670389
Updated several NGS tools to better handle stderr (allow for extremely large stderr output)
2010-03-30 16:33:19 -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
Anton Nekrutenko
175c63e0fd
Modifications to pileup_parser
2010-03-02 16:35:21 -05:00
Kelly Vincent
d091640cb5
Fixed dbkey's in sam_pileup and sam_to_bam tools in tests so they will pass
2010-02-25 23:20:19 -05:00
Nate Coraor
0bfa58679b
Fix locations of cached data for tests
2010-02-25 12:27:07 -05:00
Kelly Vincent
09fa3f0bf1
Updated Bowtie test files to handle new version (0.12.3) of Bowtie (bowtie_color_wrapper will fail until new version installed). Updated samtools tools test files. Removed version references from Bowtie and BWA tools.
2010-02-24 07:11:43 -05:00
Kelly Vincent
a314b3716b
Updated BWA wrapper, SAM to BAM, SAM Merge, and SAM Pileup so that the return code of the program is captured and if it fails, the stderr is printed; temp files are created locally; a message is printed if results file empty.
2010-02-23 10:40:19 -05:00
Daniel Blankenberg
37ae9ac29d
Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.
2010-02-05 16:06:27 -05:00
Daniel Blankenberg
561f0abf75
Have sam2interval provide a (partial) header so that strand is automatically set in metadata.
2010-02-05 11:53:06 -05:00
Anton Nekrutenko
540cfb1931
Small edit for the help section
2010-01-14 14:20:01 -05:00
Anton Nekrutenko
a4361dcce1
Modification of pileup filter behavior, bases not different from the references are included in the report as well. Also changed the image for closing screencast panels. A new icon is urgently needed.
2010-01-14 14:07:05 -05:00
Greg Von Kuster
7051ce7dd5
Rename the before_edit() and after_edit() metadata related methods to be more appropriately named before_setting_metadata() and after_setting_metadata(), and add the metthods to all datatype classes. Move sorting of Bam files from the Bam set_meta() method to this new method.
2009-12-08 09:05:35 -05:00
Greg Von Kuster
bcd6751cdf
Fix for uploading a Bam file that has not yet been sorted, the call to samtools sort has been moved from the sam_to_bam tool to the Bam()set_meta() method to ensure all Bam datasets are sorted prior to indexing. Added new functional tests to cover uploaing unsorted Bam files. Also cleaned up code in the upload tool for uploaing various binary data formats.
2009-12-07 16:04:33 -05:00
Greg Von Kuster
08e0d5e532
Fixes for Bam data type's set_meta() and sam_to_bam tool, indexes will now be properly created for bam datasets. Fixes also for uploading Bam files, they will no longer be uncompressed on upload.
2009-12-04 19:51:46 -05:00
Kelly Vincent
606ac644f3
Added some error checking to pileup_parser tool so that it exits with a meaningful message if the user tries to do some 6-column work on a 10-column file, or vice versa.
2009-12-01 16:18:25 -05:00
Kelly Vincent
0a51932168
Changed sam-to-bam test by removing nonexistent dbkey from test input specification.
2009-11-11 13:53:48 -05:00
Nate Coraor
56032de2bd
Upgrade to Cheetah 2.2.2
2009-11-10 13:47:34 -05:00
Kelly Vincent
8879adc01e
Commented out second test for SAM-to-BAM so tests will pass, because it relies on using a built-in dbkey that doesn't exist in builds.txt
2009-11-06 16:52:00 -05:00
Anton Nekrutenko
7189873b59
bug fix for pilup_parser reported by user
2009-10-06 09:44:34 -04:00
Kelly Vincent
0ffbe38fc3
Several small changes to Samtools pileup tool to get it to work with user-supplied reference genome
2009-10-05 10:35:39 -04:00
Kelly Vincent
5c94d0c273
Corrected Samtools Pileup tool to accept only BAM files as input, instead of also SAM
2009-10-02 09:37:57 -04:00
Kelly Vincent
ef2ef943ea
Fixed an error in the help section of the Sam Pileup tool config
2009-09-25 16:49:30 -04:00
Anton Nekrutenko
2e7fdf2bff
Added Cite to masthead
2009-09-25 13:58:15 -04:00
Kanwei Li
a947686b77
fix some typos for tools in folders N-Z
2009-09-25 02:06:03 -04:00
Anton Nekrutenko
b93db2deff
small help and parameter name tweaks
2009-09-24 11:55:55 -04:00
Anton Nekrutenko
cb635b8148
Tweaks plus reducing size of Assaf's icons
2009-09-21 15:40:22 -04:00
Nate Coraor