Ramkrishna Chakrabarty
58284e4848
Adding tests for vcf extract and filter tools
2011-02-28 15:03:45 -05:00
Dannon Baker
668d03ba7d
Initial commit of Mosaik and Freebayes.
2011-02-23 14:01:58 -05:00
Ramkrishna Chakrabarty
b48d817329
Adding VCF annotate and intersect tools
2011-02-22 15:31:57 -05:00
Daniel Blankenberg
882b98531c
Add a Line/Word/Character count Text Manipulation tool.
2011-02-15 17:24:24 -05:00
Daniel Blankenberg
8cd2a39cc7
Add metabolicMine datasource tool.
2011-02-09 15:42:42 -05:00
Nate Coraor
fd221725f8
Uncomment BLAST+ tools in the sample config.
2011-02-03 16:06:20 -05:00
Daniel Blankenberg
6d3d3edf19
Add YeastMine datasource tool. Site is still under development.
2011-02-01 17:29:40 -05:00
Daniel Blankenberg
d892a301e3
Add MEME tool configuration file.
2011-02-01 11:17:44 -05:00
Peter Cock
5145f81f09
Move BLAST+ suite out of NGS section (still commented out)
2010-11-25 17:08:49 +00:00
Guruprasad Anada
8b7da7ec0e
Adding a new microsatellite birth/death analyser made by Yogeshwar from Makova lab.
2011-01-17 13:59:51 -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
Ramkrishna Chakrabarty
3675235d1e
Merge with c4978fb29af5a15a7bb6e2fb83d62db982377cf9
2011-01-07 16:21:08 -05:00
Ramkrishna Chakrabarty
77c6f3ea06
FIxed the unwanted changes made in the previous commit
2011-01-07 16:19:59 -05:00
Guruprasad Anada
c0192842b7
Adding a new microsatellite tool made by Yogeshwar from Makova lab.
2011-01-07 16:19:29 -05:00
Ramkrishna Chakrabarty
f7a35e13cb
Renamed sequencer to external_service and sequencer_type to external_service_type.
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Added table to associate external services to a request type.
Enhanced UI to support selection of multiple external services for a request type.
2011-01-07 16:12:36 -05:00
Kanwei Li
cfb3e5ff6a
Tabs to spaces for tool_confs
2011-01-04 19:55:23 -05:00
Kanwei Li
767912ffb1
Add new BED-to-bigBed converter tool to convert sorted BED files into ucsc bigBed. Requires bedToBigBed in PATH.
2011-01-04 19:48:31 -05:00
Daniel Blankenberg
b9d790af55
Add CCAT ChIP-seq peak/region caller.
2011-01-03 11:15:29 -05:00
Daniel Blankenberg
2a510df4aa
Add samtools flagstat tool.
2010-12-15 23:39:16 -05:00
Nate Coraor
94273cd27f
Comment out BLAST+ tools in sample tool_conf since we do not run them on Galaxy
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Test.
2010-11-22 10:56:22 -05:00
Peter Cock
7ce54fe460
Remove FASTA filter script from BLAST+ tools (I want to generalise it)
2010-10-25 10:28:39 +01:00
Peter Cock
22fb64823a
Include BLAST-XML to tabular in tool_conf.xml.sample
2010-10-13 10:35:59 +01:00
Nate Coraor
4b5ff44d3b
Remove missing hapmapmart tool from sample tool conf
2010-11-05 14:54:36 -04:00
Kelly Vincent
c75adfdda5
Adding NGS simulation tool
2010-11-03 13:52:52 -04:00
Jeremy Goecks
f16b70c403
Add RNA-seq tools -- Tophat + Cufflinks suite -- to main.
2010-10-20 15:14:25 -04:00
Peter Cock
bed7a83e0b
Adding blastx and tblastx wrappers, tidying
2010-09-28 16:42:53 +01:00
Peter Cock
f9f223cbb3
Adding basic tblastn wrapper
2010-09-28 15:51:39 +01:00
Peter Cock
04a15b7851
Adding simple python script to split a FASTA file into those sequence with/without BLAST hits using tabular output
2010-09-28 14:43:50 +01:00
Peter Cock
7c42556467
Add basic blastp wrapper
2010-09-28 11:41:40 +01:00
Peter Cock
4078e97c8e
Adding basic NCBI BLAST+ blastn wrapper with multiple output format support
2010-09-21 18:30:13 +01:00
Daniel Blankenberg
3293abc9b4
Enable 'FASTX-Toolkit for FASTQ data' as a subsection under 'NGS: QC and manipulation' in tool_conf.xml.sample/main.
2010-10-07 09:27:34 -04:00
Richard Burhans
e6a05f3bd1
Updates to disease ontology and lps tools
2010-09-15 12:21:37 -04:00
Richard Burhans
c4ef1f8b5b
Initial checkin of Human Genome Variation tools
2010-09-14 18:20:15 -04:00
Jeremy Goecks
be23cd0629
Update main tool_conf to include GFF filtering tools and organization.
2010-09-08 12:22:21 -04:00
Daniel Blankenberg
e0b1f36bcd
Add a wig to bigWig converter tool.
2010-09-01 17:15:08 -04:00
Kelly Vincent
33bd292e41
Added BAM-to-SAM tool
2010-09-01 09:44:12 -04:00
Jeremy Goecks
bcc1e7b76c
Add tool 'gff_filter_by_feature_count', create 'GFF' subheading under Tool Menu's Filter category for GFF filtering tools, and rename 'gff_filtering' tool 'gff_filter_by_attribute.'
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gff_filter_by_feature_count tool filters a GFF file using conditions based on transcripts' features counts; for example, it is possible to filter for transcripts that have a minimum number of exons or transcripts that have 3' UTRs.
Added GFF subheading to Tool Menu under Filtering and placed all GFF filtering tools under this heading.
2010-08-26 12:00:41 -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
Guruprasad Anada
12b9c486ea
Adding wavelet analysis tools made by Zaky from Makova lab.
2010-08-16 18:30:37 -04:00
Ramkrishna Chakrabarty
37ff568432
Mutation visualization tool
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Added svgfig egg
2010-08-12 14:21:59 -04:00
Daniel Blankenberg
36f7bcb0c8
Modify tools contributed by Chungoo Park (cxp440@psu.edu) for Linear Discriminant Analysis, and drawing Receiver Operating Characteristic plots; add a new tool to 'Generate A Matrix for using PC and LDA'; remove redundant 'Principal Component Analysis' tool.
2010-07-16 14:52:52 -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
Daniel Blankenberg
ff18016e41
Add a VCF to MAF Custom Track converter tool. This tool converts a Variant Call Format (VCF) file into a Multiple Alignment Format (MAF) custom track file suitable for display at genome browsers.
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This file should be used for display purposes only (e.g as a UCSC Custom Track). Performing an analysis using the output created by this tool as input is not recommended; the source VCF file should be used when performing an analysis.
Unknown nucleotides are represented as '*' as required to allow the display to draw properly; these include e.g. reference bases which appear before a deletion and are not available without querying the original reference sequence.
2010-06-14 15:07:46 -04:00
Daniel Blankenberg
a0b41dc0a9
Update tool_conf.xml.* to only use the generic python FASTQ to FASTA converter by default.
2010-06-10 09:25:37 -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
Kelly Vincent
f9f54848ed
Add SAM indel filter tool to tool_conf.xml.sample
2010-06-07 15:30:20 -04:00
Greg Von Kuster
15abe33231
Add the CBI Rice Mart data source tool to the distribution.
2010-06-04 15:49:58 -04:00
Daniel Blankenberg
1d87c0c5d4
Add tools contributed by Chungoo Park (cxp440@psu.edu) for Principal Component Analysis, Linear Discriminant Analysis, and drawing Receiver Operating Characteristic plots.
2010-05-25 15:48:25 -04:00
Ross Lazarus
3ebeb02d89
Branch merge
2010-05-23 08:45:01 -04:00
Ramkrishna Chakrabarty