Greg Von Kuster
f16d27c2d4
Add datasource tool configs for modMine and Ratmine.
2009-12-03 15:33:15 -05:00
Guruprasad Anada
10af4c5ccf
Adding back 'wiggle to interval' converter
2009-12-01 11:49:07 -05:00
Greg Von Kuster
20628e8381
First pass of the lastz tool wrapper that includes job splitting - works but needs polishing.
2009-11-27 10:53:50 -05:00
Nate Coraor
bdce4bb21e
Remove tool conf typo
2009-11-06 14:36:36 -05:00
Nate Coraor
607d670872
Add Genetrack tools and display site
2009-11-06 14:22:44 -05:00
Anton Nekrutenko
103b168a1e
added space to paste tool, removed old solexa tool, fixes fastq stat test
2009-10-08 09:01:19 -04:00
Anton Nekrutenko
809f774f36
ngs updates
2009-10-07 11:18:14 -04:00
Kelly Vincent
91de8aceb4
Added FASTQ \"Groomer\" tool to converters section. Relies on new datatype (fastq) which will be added later.
2009-10-06 21:25:01 -04:00
Anton Nekrutenko
aaff3baf52
Added text trimmer that can be used to groom fastq data
2009-09-30 14:11:01 -04:00
Anton Nekrutenko
13c7b84abb
Second pass of help and interface updates. Not done yet...
2009-09-22 08:59:36 -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
Kelly Vincent
32b6cb88f5
Added pileup-to-interval tool to tool_conf.xml.sample
2009-09-18 13:58:43 -04:00
Nate Coraor
ff9f7a62b8
lastz commented as per Anton's instructions, the wrapper and params will be rewritten shortly.
2009-09-18 13:45:14 -04:00
Anton Nekrutenko
1ccbc4e736
getting rid of maq
2009-09-18 10:40:53 -04:00
Anton Nekrutenko
efaf4ecc00
Forgot Ross' tools
2009-09-18 10:29:34 -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
Kelly Vincent
248a16e962
tool_conf.xml.sample for added BWA wrapper tool
2009-09-16 11:27:50 -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
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
e13eaf8a0c
Added Bowtie wrapper tool
2009-09-11 14:38:05 -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
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
Kelly Vincent
5d4b1151d0
Added solid_to_fastq and fastq_conversions converters to Convert Formats section
2009-07-31 11:48:37 -04:00
Kelly Vincent
b6ea9ed1eb
Added BWA wrapper tool to Short Read Mapping Tools
2009-07-24 15:13:11 -04:00
Greg Von Kuster
0090622f59
Add ability to share histories with multiple users, along with bug fixes and more functional test coverage for history features.
2009-06-05 11:15:25 -04:00
Greg Von Kuster
e608f904ee
Add tool config for GrameneMart data source.
2009-05-27 14:19:59 -04:00
Guruprasad Anada
24293166da
MAQ mapping pipeline for SOLiD data
2009-05-13 21:54:45 -04:00
Guruprasad Anada
4f1a6fe60f
Added SOLiD tool section with QC tools.
2009-05-05 22:44:30 -04:00
Anton Nekrutenko
7b5136a4c0
Changed taxonomyu to metagenomics
2009-03-02 14:52:59 -05:00
Guruprasad Anada
6fd54350eb
Integration of Assaf Gordon's Solexa toolkit into Galaxy - (all tools except 3 are working fine).
2009-02-20 14:17:46 -05:00
Anton Nekrutenko
19bb2c924c
A simple tool for merging columns. Surprisingly useful for some analyses and also requested by a user lest Friday
2009-02-09 23:57:41 -05:00
Ian Schenck
82d09f5824
Finally remerged changeset. Should be good now.
2009-01-21 16:48:54 -05:00
Nate Coraor
427bc02028
Backed out changeset 83a0c394a797
2009-01-21 16:03:59 -05:00
Ian Schenck
73d609cf31
Merged
2009-01-21 11:45:50 -05:00
Anton Nekrutenko
42adeabbc9
Lca commit. The tool itself is written by guru with minor modification made by me.
2009-01-21 09:51:06 -05:00
Ian Schenck
6a0aa166aa
Initial GeneTrack commit. Most parts are in, but dependencies will still be a problem.
2009-01-19 17:45:28 -05:00
Greg Von Kuster
051a78bc39
Add new tool config for flymine production server.
2009-01-13 10:55:08 -05:00
Greg Von Kuster
42ca95a373
Enhance the tool panel, now supports following tags:
...
<toolbox>
<tool file="data_source/upload.xml"/> # tools outside sections
<label text="Basic Tools" id="basic_tools" /> # labels outside sections
<workflow id="529fd61ab1c6cc36" /> # workflows outside sections
<section name="Get Data" id="getext"> # sections
<tool file="data_source/biomart.xml" /> # tools inside sections
<label text="In Section" id="in_section" /> # labels inside sections
<workflow id="adb5f5c93f827949" /> # workflows inside sections
</section>
</toolbox>
2008-12-18 16:35:26 -05:00
Greg Von Kuster
dfd5e9827f
Rename gbrowse_elegans to wormbase_test, add a config for the wormbase production server.
2008-12-15 10:37:39 -05:00
Greg Von Kuster
7b49309886
Add new EpiGRAPH tools that point to EpiGRAPH production server.
2008-10-28 11:27:42 -04:00
Wen-Yu Chung
0021c40c85
add shrimp_color_space mapping tool with functional test data.
...
add a new datatype called csfasta.
2008-10-13 15:06:42 -04:00
Greg Von Kuster
b3b6c54247
Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).
2008-10-07 15:21:46 -04:00
Greg Von Kuster
c05f66d5ee
Treat EpiGRAPH as a data source much like ucsc table browser.
2008-10-06 13:34:51 -04:00
Guruprasad Anada
0f1130e84a
Adding tools to fetch microsatellites and estimate their mutabilities.
2008-09-24 18:20:39 -04:00
Greg Von Kuster