Daniel Blankenberg
8a6b0001c2
Minor fix for 04e8ed0cd930.
2011-11-29 17:35:14 -05:00
Daniel Blankenberg
023c4db69e
Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.
2011-11-29 17:30:14 -05:00
Daniel Blankenberg
8b402babb2
Update SRMA wrapper to use data tables.
2011-10-31 09:49:51 -04:00
Jennifer Jackson
2ff5dcfb33
Other genome description: corrected typo.
2011-10-10 18:42:31 -04:00
Jennifer Jackson
a1d4bb9bab
Other genome description: revised all, corrected canonical male
2011-10-10 18:33:48 -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
Kelly Vincent
c565726192
Updated help section of BWA wrappers to include tags for the RG header record type
2011-05-12 13:38:00 -04:00
Kelly Vincent
9eaf2ec821
Updated SRMA to properly set dbkey and changed functional tests so that they can handle a single line difference for the SRMA version number tag
2011-05-11 10:49:32 -04:00
Kelly Vincent
78a4a14131
BWA enhancements: added new options to support v. 0.5.9 (-n and -r for samse/sampe and -N for sampe only); fixed dbkey setting; set Sam header suppression off by default
2011-05-09 16:37:13 -04:00
Kelly Vincent
0017486eaa
Sam header suppression made optional in BFAST and default set to off for BFAST and Bowtie. Fixed dbkey setting on outputs for for BFAST, Bowtie, Mosaik. Fixed sorting of built-in builds for these tools so ordered by pretty name.
2011-05-09 12:11:54 -04:00
Nate Coraor
1fdfacc977
Set the ftype of SRMA test outputs so the BAMs are compared as SAMs
2011-03-23 10:59:26 -04:00
Kelly Vincent
a4f910c730
Update SRMA test files so that functional tests pass
2011-03-08 16:17:09 -05:00
Daniel Blankenberg
4685ec3f8a
Enhance Bowtie wrapper to accept non-sanger variant FASTQ files.
2011-03-02 11:40:58 -05:00
Dannon Baker
a9548d1a07
Remove ftype from mosaik/freebayes test outputs.
2011-03-02 08:38:19 -05:00
Nate Coraor
cb9bbd0e0b
Update bwa_color_wrapper cached indices name to match the key used in the test data repository
2011-03-01 15:21:25 -05:00
Dannon Baker
48b65e9b17
mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag.
2011-02-28 14:32:36 -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
Dannon Baker
11f15b123b
Freebayes and Mosaik updates
2011-02-25 17:53:58 -05:00
Kanwei Li
096e95ff41
Typos
2011-02-25 13:35:27 -05:00
Dannon Baker
668d03ba7d
Initial commit of Mosaik and Freebayes.
2011-02-23 14:01:58 -05:00
Nate Coraor
7ef6723533
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.
2011-02-23 13:54:06 -05:00
Nate Coraor
f501a13c53
Update bowtie_wrapper and bowtie_color_wrapper to use test data from the external test data repository
2011-02-21 16:25:35 -05:00
Kelly Vincent
c0726bfb23
Fixed BFAST functional tests (corrected problem with chromosome names in test files)
2011-02-17 13:46:40 -05:00
Kelly Vincent
64553e62fa
Removed errant right parenthesis from BFAST wrapper command
2011-01-14 00:23:15 -05:00
Kelly Vincent
6964db79f2
Added paired-end reads functional tests for BWA color-space and base-space wrappers
2011-01-13 14:33:04 -05:00
Kelly Vincent
11a00ec694
Added description to two BWA wrappers to distinguish between color-space version and base-space versions
2011-01-12 13:47:01 -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
Kelly Vincent
76b3cb5844
Added BWA color space wrapper; fixed names of FASTQ test files to indicate data type
2011-01-12 12:13:54 -05:00
Daniel Blankenberg
0adf8f72c3
Change method of accessing additional fields by name for dynamically generated select lists which was added in 4784:7be369e7cc6f.
...
Access now takes the form similar to ${param.fields.path}.
2011-01-05 14:57:05 -05:00
Daniel Blankenberg
93925d842e
Update bfast wrapper to use $param.get_field( "path" ) method instead of previous hack to access path when building the command-line.
2011-01-03 10:38:00 -05:00
Daniel Blankenberg
7ad8a9a446
Remove erroneous "Unmapped Reads" label from bfast output which appeared in 4696:3b3b7f382ee2.
2010-12-20 15:58:31 -05:00
Daniel Blankenberg
38429a93b0
Fix for reversion of 4666:b45e2439ff05 which occurred in 4696:3b3b7f382ee2. Re-fixes setting of output dbkey when pre-built indexed datasets are used.
...
Original FIXME still stands.
2010-12-15 12:13:19 -05:00
Kelly Vincent
f61d147034
Added --max and --un file output options to Bowtie and modified tests to test for them.
...
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
Daniel Blankenberg
e42b3e1b01
Update bowtie tool output dataset actions to reference columns in the new location file style.
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FIXME: Tool output actions need to be made data_table aware.
2010-11-22 16:02:43 -05:00
Nate Coraor
246ea04cc7
Add support for the new test/data repository and a fix for the bowtie tests.
2010-11-22 10:54:31 -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
7d0ff14df9
Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.
2010-11-08 00:10:13 -05:00
Daniel Blankenberg
db737b3003
Add basic support for bowtie indexes as a datatype (bowtie_base_index, bowtie_color_index), available via datatype conversion. Currently, the indexes need to be converted manually from the FASTA file before use in bowtie, but they can be reused.
...
More work is required to allow the one-off indexes built by bowtie to become Galaxy datasets; alternatively, the custom genome selection could be limited to the index datatype for input (and not allow fasta directly), which would allow implicit datatype conversion to occur when a fasta file is selected as input, but this would prevent the index tuning that is currently available when currently selecting a fasta file.
2010-10-07 16:59:41 -04:00
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
James Taylor
f2b8793371
Adding requirement tags to bowtie and MACS
2010-09-26 17:28:58 -04:00
James Taylor
37673ac124
Initial support for tool dependencies.
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Enabled only if tool_dependency_dir is set in universe_wsgi.ini. Packages
should be installed under this directory organized by name and version.
Each package directory should contain an sh script that can be sourced
to make that package available in the current shell environment (by setting
PATH, PYTHONPATH, LD_LIBRARY_PATH, ...).
If a requirement tag of type 'package' is found in a tool, Galaxy will
try to find a directory corresponding to the name and version of the package.
If no version is provided, it will look for the version 'default' which should
always be a symbolic link to a real version.
Actually adding the paths is currently only implemented in the local runner.
Currently, if a dependency cannot be found, running continues without it, so
this should be completely backward compatible with existing installations
even as more requirement tags are added.
2010-09-25 20:21:04 -04:00
Kelly Vincent
d1d106508a
Don't use unsanitized parameters in BWA, Bowtie, and PerM wrappers
2010-09-16 11:19:08 -04:00
Kelly Vincent
1cbda4c6c7
Corrected bug in parameter specification for Lastz full parameter setting
2010-09-09 12:28:04 -04:00
Kelly Vincent
6d2b2acf1b
Issue #380 : Properly handle -n and -v options in Bowtie
2010-08-31 01:04:32 -04:00
Kelly Vincent
3b12bb72e9
Fixing buildbot tests: added missing column join test files; regenerated and enhanced BWA test files; sorted tophat_out1.sam and specified sort=True in test for it
2010-08-25 21:51:41 -04:00
Kelly Vincent
f6a3996d9b
Adding SRMA wrapper and all associated test files and index loc sample
2010-08-19 18:17:31 -04:00
Daniel Blankenberg
94c7417f37
Add BFAST Mapper tool and wrapper.
2010-08-18 16:52:06 -04:00
Daniel Blankenberg
b951bdd727
Add ToolOutputActions to set dbkey for BWA wrapper and remove no longer needed code file.
2010-08-10 11:36:50 -04:00
Daniel Blankenberg