Anton Nekrutenko
b93db2deff
small help and parameter name tweaks
2009-09-24 11:55:55 -04:00
Daniel Blankenberg
4142fc75fe
Changing an 'and' to 'or' in SNP mutate codon tool error checking.
2009-09-22 11:40:41 -04:00
Daniel Blankenberg
97297d4e3a
More friendly error reporting for mutate SNP codon tool.
2009-09-22 11:37:41 -04:00
Kelly Vincent
eecf0af42b
Modified Concatenate queries tool to have two base files to concatenate and the option to add a third or more. Also removed to unnecessary sort1 test files.
2009-09-22 10:09:23 -04:00
Anton Nekrutenko
13c7b84abb
Second pass of help and interface updates. Not done yet...
2009-09-22 08:59:36 -04:00
Kelly Vincent
33ad975b3f
Modified sort to allow sorting by multiple columns
2009-09-21 17:02:26 -04:00
Anton Nekrutenko
cb635b8148
Tweaks plus reducing size of Assaf's icons
2009-09-21 15:40:22 -04:00
Anton Nekrutenko
8d0e39c9f8
More SR changes
2009-09-21 10:32:48 -04:00
Guruprasad Anada
edd8093627
Commenting out functional test for fastx_collapser tool as the order of sequences in the output seems to differ between 32 bit and 64 bit machines.
2009-09-18 15:48:06 -04:00
Guruprasad Anada
ab8f07fe9c
Fixed a bug in fasta_formatter tool test case, which was causing the functional tests to fail.
2009-09-18 15:28:18 -04:00
Guruprasad Anada
739e786bc1
Adding qualsolid_boxplot_graph.sh script used by SOLiD quality boxplot tool to the distribution.
2009-09-18 14:21:59 -04:00
Kelly Vincent
bbfde2c0cd
Added header removal option to BWA wrapper tool, and cleaned up its test files. Also added the bwa_solid2fastq_modified.pl script to the next gen conversion directory for the solid-to-fastq tool.
2009-09-18 12:11:43 -04:00
Anton Nekrutenko
2105021def
small tweaks
2009-09-18 11:11:41 -04:00
Anton Nekrutenko
eaed01bcf4
First pass of consolidating NGS tools
2009-09-18 10:27:03 -04:00
Kelly Vincent
be211aa254
Added the Pileup-to-Interval tool to condense pileup format
2009-09-18 10:15:09 -04:00
Daniel Blankenberg
7cd1c6dfd0
Add a MAF to Interval converter that produces a set of intervals with sequence data.
2009-09-17 11:47:37 -04:00
Anton Nekrutenko
75ce85cd3f
Added sam2interval converter
2009-09-16 16:00:09 -04:00
Anton Nekrutenko
b833f1819d
A tool for filtering SAM datasets on bitwise flag.
2009-09-16 15:19:35 -04:00
Guruprasad Anada
e6e5bd24b5
fastx_clipper tool config problem resolved
2009-09-16 14:55:55 -04:00
Kelly Vincent
45201c6054
Updated BWA wrapper tool: replaced threads option to hard-coded value, changed output and test file output datatype to sam, changed test file names to standard, better cleanup of temp files, added dbkey parameter and exec_before_job method to set it. Also changed name of a FASTQ Conversions tool test file
2009-09-16 11:14:39 -04:00
Kelly Vincent
db273d3c2d
In Bowtie wrapper tool, removed --quiet option and redirected stderr to /dev/null
2009-09-15 14:26:20 -04:00
Daniel Blankenberg
132376998d
Add a new tool, Mutate by SNP codon, which will take codon position and sequence information that is joined to SNP data and create a 'mutated codon'.
2009-09-15 12:04:14 -04:00
Guruprasad Anada
3877665d26
More modifications to fastx toolkit: added fastqsanger to input format list and changed the ascii offset param to select.
2009-09-15 11:28:50 -04:00
Anton Nekrutenko
c4b8764d6f
Modification for input datatype in the splitter:w
2009-09-15 10:30:54 -04:00
Guruprasad Anada
7a978e7ce8
Updating FASTX tool-set to the latest version v0.0.10
2009-09-14 17:03:17 -04:00
Anton Nekrutenko
28ccd18f7d
Modifications for fastq splitted help
2009-09-14 15:27:55 -04:00
Kelly Vincent
f2aaa29988
Updated Bowtie wrapper tool to add a number of threads parameter and remove two unnecessary options
2009-09-14 14:54:11 -04:00
Kelly Vincent
e13eaf8a0c
Added Bowtie wrapper tool
2009-09-11 14:38:05 -04:00
Guruprasad Anada
140b458dbb
Bug fix for 'Fetch closest feature' tool.
2009-09-10 17:35:21 -04:00
Nate Coraor
6f3a169b01
Get rid of the hacky "alternate path" stuff used by the upload tool and fix setting metadata when using autodetect and set_metadata_externally
2009-09-10 14:52:38 -04:00
Daniel Blankenberg
c8ddfaaadb
Fix heading for Example 2 in maf_split_by_species onscreen tool help.
2009-09-04 11:08:10 -04:00
Daniel Blankenberg
6de4ac1c27
removing debuging statements from annotation_profiler that were never inteded to go out
2009-09-04 10:49:02 -04:00
Daniel Blankenberg
87eebd3206
First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.
...
These changes should only affect output when an input block has a species appearing more than once, with the exception being the MAF to multiple FASTA blocks converters: the FASTA headers have been revised to included the sequence index for a species in a block as well as the block index.
A new tool "Split MAF Blocks by Species" has been added that will split MAF blocks into the complete combination of multiple blocks when a species appears more than once.
2009-09-04 10:40:16 -04:00
Anton Nekrutenko
61c7d63087
Added pileup parser. Pardon the perl = used to its regexes too much
2009-09-04 10:23:37 -04:00
Guruprasad Anada
13ef14c6dd
Added a new option to 'fetch closest features' tool to return the closest feature either upstream or downstream.
2009-09-02 13:36:16 -04:00
Kelly Vincent
1008d8692f
Added several options to the Samtools pileup tool
2009-09-01 17:01:44 -04:00
Kelly Vincent
9d0dd5f7ce
Added samtools-based tools (sam_to_bam, sam_merge, sam_pileup) with their supporting files and modified Bam datatype so temp files are properly cleaned up
2009-08-28 15:59:16 -04:00
Nate Coraor
2e407c0b21
Fix for multi-byte file uploads
2009-08-25 14:58:37 -04:00
Nate Coraor
4158ee0833
set job state to new in upload tool action so that track_jobs_in_database works
2009-08-25 11:53:42 -04:00
Guruprasad Anada
d72d1a7205
Change dbkey of unmapped liftover dataset to the input dataset's dbkey.
2009-08-21 11:40:51 -04:00
Anton Nekrutenko
bf9666bf21
Fixed a stupid and truly horrible paired end splitter bug
2009-08-20 17:33:39 -04:00
Nate Coraor
3f5da01132
Real Job(tm) upload support
2009-08-20 10:49:54 -04:00
James Taylor
95100849be
Merge.
2009-08-19 17:51:46 -04:00
Kanwei Li
e63bd72334
Typo
2009-08-19 11:33:58 -04:00
Greg Von Kuster
d0d7875192
Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.
2009-08-14 15:37:31 -04:00
Daniel Blankenberg
b1fbae947b
Testing framework will now click the add button for nested repeats when repeat content has been specfied.
2009-08-05 11:54:34 -04:00
Daniel Blankenberg
0e651adbe1
Allow nested groupings in testing framework.
2009-08-05 08:58:23 -04:00
Kelly Vincent
f5d67cda72
Renamed test files and fixed output datatype problem with solid-to-fastq tool
2009-08-04 16:32:57 -04:00
Kelly Vincent
57f0f10d38
Commented out failing test in solid_to_fastq and added test files that fastq_conversions relies on
2009-08-03 16:58:22 -04:00
Guruprasad Anada
bcd0192709
Fix bar chart output format.
2009-08-03 16:38:27 -04:00
Anton Nekrutenko