Nate Coraor
87db3952d3
Real Job(tm) support for the library upload tool. Does not include iframe upload for the library side yet.
2009-09-25 14:36:12 -04:00
Anton Nekrutenko
2e7fdf2bff
Added Cite to masthead
2009-09-25 13:58:15 -04:00
Guruprasad Anada
cb875eae2e
Fix functional test for fastx_artifacts_filter tool.
2009-09-25 10:45:10 -04:00
Kanwei Li
a947686b77
fix some typos for tools in folders N-Z
2009-09-25 02:06:03 -04:00
Kelly Vincent
1b0c05e257
Modified solid to fastq converter tool to specify path to perl script that does conversion
2009-09-24 14:09:17 -04:00
Kelly Vincent
52b8b0b667
Modified sort tool to fix backwards compatibility. Reverted catWrapper tool back to old version before recent changes (for backwards compatibility).
2009-09-24 13:54:12 -04:00
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
Nate Coraor