Daniel Blankenberg
11fd8d08e4
Add RViewer external display application.
2012-02-17 10:00:42 -05:00
Daniel Blankenberg
a25dbe5603
GATK: add newly introduced gatkreport datatype, currently used by variant eval.
2012-01-27 10:46:58 -05:00
Nate Coraor
943ce1de96
Merged in jdlogicman/galaxy-central-add-xml-mimetype (pull request #16 )
2012-01-23 14:34:38 -05:00
Greg Von Kuster
651f0a7024
Eliminate all references and support for datatype indexers since they have never been used - datatype converters do the same thing.
2012-01-06 15:43:35 -05:00
Daniel Blankenberg
08013f4ef1
Add UCSC VCF external display application.
2011-12-20 15:40:07 -05:00
Daniel Blankenberg
cc38aae783
Add Picard Interval List to BED6 converter.
2011-12-16 14:39:40 -05:00
Jeremy Goecks
2c68904b30
Add automatic conversions for SAM to BAM and SAM to summary tree. Enable SAM datasets to be visualized in Trackster.
2011-12-06 09:34:19 -05:00
Daniel Blankenberg
8986dc2c81
Add SAMTools mpileup.
2011-11-21 16:30:34 -05:00
Daniel Blankenberg
09bcf6e95a
Add VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix).
2011-11-15 17:24:38 -05:00
Daniel Blankenberg
0f98fc6814
Add 'type_extension' attribute to datatypes_conf.xml that allows creating a datatype from an earlier declared datatype by referencing extension. Make several datatypes that had been direct instantiations from Data become subclasses of Binary.
2011-11-15 14:28:08 -05:00
John Duddy
39f5a3995d
Add support for generic XML files for tool integrations
2011-10-31 17:16:17 -07:00
John Duddy
642688263c
add FQTOC datatype to drive file splitting
2011-10-10 12:17:57 -07:00
Kanwei Li
fec37cd896
Standardize {datatypes|tool}_conf.xml.sample with 2 space indentation and newline before <label> blocks
2011-10-04 23:29:08 -04:00
Jeremy Goecks
5b3561444d
Enable Trackster to use and display custom build data and update datatypes_conf sample to include converters for custom build datasets.
2011-09-21 11:11:08 -04:00
Jeremy Goecks
a7c2899448
Use fasta HDAs to specify custom builds. Do automatic conversions from fasta to 2bit and len; also, do conversion from len to linecount so that chrom/contig count is available. Finally, refactor 'compute fasta length' code out of tools and into converters.
2011-09-20 11:19:44 -04:00
Daniel Blankenberg
d301e2cd57
Update existing GATK tools. Add 4 new GATK tools: VariantAnnotator, VariantFiltration, VariantRecalibrator, ApplyRecalibration, ValidateVariants, VariantEval and CombineVariants. All GATK tool wrappers are still considered BETA and (workflow/rerun/etc) backwards-incompatible changes should be expected.
2011-09-01 11:08:34 -04:00
Daniel Blankenberg
8768351b99
Add FIMO tool from MEME suite.
2011-08-22 14:52:11 -04:00
Greg Von Kuster
d8279f0e5c
Add an altered version of Jelle Scholtalbers' enhancement code to support uploding various image data types. I've moved some of the code components around from Jelle's version, and added some fixes. The cod ein the new image_util.py file enables detections of images types without the need to create a new Image() class.
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I've also added baseline support of the HDF5 data type in this change set, but it is currently required to be in the unsniffable_data_types list.
2011-07-27 16:14:15 -04:00
Trevor Wennblom
424aca090e
minor whitespace updates, tab/space consistency
2011-07-22 15:17:26 -05:00
Kanwei Li
0d3425ee81
Sniffers: Fix sniffers not being loaded from datatypes.conf file. Modify VCF sniffer to just check a simple header string.
2011-06-14 13:22:12 -04:00
Peter van Heusden
1f6d9fe5e4
Added TwoBit datatype for twobit binary nucleotide datatype. Sniffer code
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based on bx-python's bx.seq.twobit.
2011-06-13 14:05:41 +02:00
Kanwei Li
f2286c240a
BLAST: Fix sniffer for some dataset. Closes #567 . Set mimetype to application/xml. Closes #569
2011-06-02 17:36:38 -04:00
Daniel Blankenberg
364180ef7d
First pass at adding some GATK tools. Included tools are "Realigner Target Creator", "Indel Realigner", "Count Covariates", "Table Recalibration", "Analyze Covariates" and "Unified Genotyper". These tool integrations should be considered beta: changes that will not be backwards-compatible with workflows and re-run functionality should be expected.
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TODO:
A few new datatypes have been declared, but exist in name only (subclasses of Text defined only in datatypes_conf.xml), these should be refined to be true datatypes, with proper peeks, sniffing, metadata, etc.
Help sections need work.
HTML listing of files in e.g. Analyze Covariates should be prettified.
Other items not listed.
2011-05-11 09:38:23 -04:00
Kanwei Li
2e3c767ec4
trackster: Restore interval_index as Gff indexer for now due to sorting issues
2011-04-27 19:08:31 -04:00
Kanwei Li
43de1e17ce
Fix GTF for trackster
2011-04-27 15:41:25 -04:00
Kanwei Li
8e2f6f4c8f
trackster:
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- Make GFF, Bed and Vcf use Tabix data provider instead of interval_index. PLEASE UPDATE with new entries in datatypes_conf.xml.sample
- Refactoring for data providers
2011-04-25 18:59:37 -04:00
Richard Burhans
d3b7aaeb6b
initial version of Webb's genome diversity tools
2011-04-21 17:22:27 -04:00
Kanwei Li
b2ba5d422a
trackster:
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- Use tabix (through pysam) as the indexer for feature formats. Bed support included in this commit
- Add bigBed format support (same interface as bigWig)
- Improve implicit converter error handling
2011-04-18 18:07:52 -04:00
Kanwei Li
fc550cdbab
Remove array_tree datatype; add tabix
2011-03-31 18:58:02 -04:00
Daniel Blankenberg
d95c6b2e52
Add IGV as an external display application. Contributed by Tobias Wohlfrom.
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Provides two links for IGV:
1) web - to view with Java web start IGV if the user has no IGV installed
2) local - to view in the user's running IGV instance (requires remote port enabled in IGV)
2011-03-23 09:57:06 -04:00
Daniel Blankenberg
d892a301e3
Add MEME tool configuration file.
2011-02-01 11:17:44 -05:00
Jeremy Goecks
9d34f038b2
Add GTF sniffer to datatypes config sample file.
2011-01-31 18:25:33 -05:00
Kanwei Li
5962f0ab2e
trackster: Add bigWig display to trackster. Automatically converts wig to bigwig if needed (NOTE: datatypes_conf.xml.sample has been edited to add the new converter, you must update datatypes_conf.xml to use it). The converter requires that wigToBigWig be in the PATH, but no other tools are needed to view bigwig files as they are provided by bx_python.
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- Fix track preferences not being applied
- Fix chroms not being selectable when a new track browser is created
- Fix ReferenceTrack not working with filters
- Fix visual analytics error when tool configuration has changed
2010-12-10 14:59:43 -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.
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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
Jeremy Goecks
9c7065d898
Make VCF (variant call format) a Galaxy datatype and enable very basic VCF support in trackster. VCF datatype is sniffable and can be converted to summary tree and interval index. In trackster, VCF files are represented as single-base pair feature tracks.
2010-10-06 16:23:55 -04:00
Brad Chapman
8679ac8442
Add support for displaying BAM files at Ensembl
2010-10-06 11:03:28 -04:00
Ramkrishna Chakrabarty
5219ada91e
added svg datatype
2010-08-25 12:27:24 -04:00
Greg Von Kuster
a7e30c4441
Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.
2010-08-19 13:58:10 -04:00
Daniel Blankenberg
063b5c5381
Add new-style display applications for GBrowse for gff, interval, and wig; only interval is enabled by default, the other two use existing methods. Still working on SAM and BAM for GBrowse.
2010-07-23 16:45:41 -04:00
Jeremy Goecks
bd1033e0e8
New feature: GFF files can be viewed in trackster. Specific additions: (a) generalized bed-to-summary-tree converter and bed-to-interval-index converter to handle both BED and GFF files and renamed accordingly; (b) augmented trackster to provide payload data from both BED and GFF files.
2010-07-14 09:26:26 -04:00
Kanwei Li
810c2291de
Detect pdf files on upload [Brad Chapman]. Resolves #357
2010-07-02 18:10:45 -04:00
Nate Coraor
7c71894533
Remove obsolete binseq.zip and txtseq.zip formats, and allow for uploading single files in a zip archive. Adapted from a patch from Pablo Cingolani.
2010-06-23 16:48:13 -04:00
Daniel Blankenberg
2603f7efc2
Add mafcustomtrack datatype and a UCSC external display application which can be used to view this datatype at UCSC.
2010-06-14 15:05:07 -04:00
Greg Von Kuster
ae749436e0
Add support for velvet data types and velveth and velvetg tool wrappers, all contributed by James E Johnson - University of Minnesota.
2010-06-09 11:23:10 -04:00
Daniel Blankenberg
169a4d2f05
First pass at implementing a method for allowing a maximum file size cutoff for setting optional metadata (e.g. line and sequence counts). Currently csFasta, qualsolid, and fastq make use of this option.
2010-05-24 14:15:02 -04:00
Daniel Blankenberg
ab53cc6d3b
First pass at adding Ensembl browsers as an external display application. Two different URL generation and data attachment methods are used; one for 'old' Ensembl archives older than ~November 2008 and another for Ensembl sites using the current method. The tool-data/shared/ensembl/ensembl_sites.txt file contains the site and build information for using the current method; the tool-data/shared/ensembl/ensembl_sites_data_URL.txt file has the site and build information for when the older method is to be used.
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The new method follows: http://www.ensembl.org/info/docs/webcode/linking.html
The old method follows: http://aug2007.archive.ensembl.org/Homo_sapiens/helpview?se=1;kw=urlsource
2010-05-21 15:25:56 -04:00
Ross Lazarus
d61fd8c4df
Added ldindep datatype to datatypes sample
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Added snpwga tool sections to tool_conf.sample.main - need these
2010-05-20 14:16:08 -04:00
Daniel Blankenberg
f08c5cd9ec
Add eland and elandmulti formats. Enhance MACs peakcaller to properly handle these formats.
2010-04-27 10:59:46 -04:00
Jeremy Goecks
e77c308f4f
Add GTF file format to Galaxy. GTF format is an extension of GFF format that is used by Tophat and Cufflinks tool suite.
2010-04-19 11:14:19 -04:00
Kanwei Li
34518df336
Add BedGraph datatype (wiggle-like data for intervals)
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trackster:
- Fix various UI issues
- BedGraph -> array_tree converter
2010-04-06 19:00:39 -04:00
Daniel Blankenberg