Greg Von Kuster
666de20b4d
Cleanup for fastqsolexa data type converters. We are currently supporting only the Solexa variant and will add support for other variants when the formats stabilize.
2008-06-09 20:15:04 +00:00
Greg Von Kuster
1a23f9e55d
Requires config modification - Add Fastq sniffer, add support for fastqsolexa data type, rename convert_fatsq2fasta tool to be fastq_to_fasta_qual, add functional tests for both fastq and fastqsolexa data types, misc code cleanup.
2008-05-29 19:12:36 +00:00
Greg Von Kuster
051dc9ca94
A bit of cleanup, added FASTQ to FASTA converted to tool_conf.xml.sample.
2008-05-27 19:59:33 +00:00
Greg Von Kuster
c32f87624f
Added code for integration with C. Elegans / GBrowse test server.
2008-05-12 18:55:48 +00:00
Greg Von Kuster
185b4353c2
Deleted findcluster_mysql tool code.
2008-05-01 17:44:56 +00:00
Anton Nekrutenko
a3ee9be735
More clean up and modification of FASTA tools
2008-04-29 14:36:04 +00:00
Greg Von Kuster
5657e61320
Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.
2008-04-25 13:04:55 +00:00
Daniel Blankenberg
7f89a78f35
Add tool for profiling locally cached annotations from the UCSC table browser.
2008-04-09 17:34:35 +00:00
Wen-Yu Chung
b8265695d2
add a new tool (poisson2test) with funcitonal test data to taxonomy section.
2008-04-08 15:05:43 +00:00
Wen-Yu Chung
67986d25f6
sorry, hit the wrong button (want to click cancel but click ok instead).
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add two tools and functional test data for short reads.
update tool_conf.xml.sample.
2008-03-31 19:29:00 +00:00
Wen-Yu Chung
163e4bc200
2008-03-31 19:24:56 +00:00
Wen-Yu Chung
598462643a
update ucsc builds.txt. now blat tool should pass functional test.
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also update boxplot config file.
2008-03-28 16:07:00 +00:00
Wen-Yu Chung
9adee0844d
update short reads tools. add functional test data.
2008-03-27 22:11:18 +00:00
Daniel Blankenberg
3025531e0b
Add a tool that allows species based concatenation of FASTA files. Useful for manipulating the results of MAF to FASTA conversion or stitching.
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This does not work on the results of the Extract Genomic DNA tool, since it uses a different header style.
2008-03-27 17:58:47 +00:00
Anton Nekrutenko
41769817da
more tax fixes
2008-03-21 15:15:11 +00:00
Anton Nekrutenko
2d14d029ea
Added taxonomy to tool_comf.xml.sample
2008-03-20 19:54:32 +00:00
Guruprasad Anada
89bb493d3c
Adding new tool to estimate insertion and deletion rates from 3-way alignments.
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Also, modified 'Fetch Indels' tool.
2008-03-13 16:21:39 +00:00
Guruprasad Anada
b032b71bc0
Adding tool to fetch closest upstream and downstream features for a given set of intervals.
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Added: Tool xml and py files, test data.
Modified: tool_conf.xml.sample.
2008-03-05 20:08:01 +00:00
Greg Von Kuster
135c9a0377
Removed the remainder of the tool version subdirectories.
2008-03-03 18:38:57 +00:00
Greg Von Kuster
4dd1f044e1
Removed tool version directiories for some of the tools...the rest soon.
2008-03-03 16:14:06 +00:00
Greg Von Kuster
335ebef0af
Restored version 1.1.0 of aggregate scores tool and moved the fixes to version 1.1.1.
2008-02-28 00:08:05 +00:00
Wen-Yu Chung
5b4e5a772b
modify data structure used in short read tools.
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update functional test data.
2008-02-25 18:42:39 +00:00
Anton Nekrutenko
f607e77b6a
Tool for changing case
2008-02-25 15:15:18 +00:00
Greg Von Kuster
9262212acd
Added tool version directories for validation and visualization tools directories.
2008-02-22 20:36:20 +00:00
Greg Von Kuster
78b2d4b78e
Added tool version directories for stats tools directory.
2008-02-22 20:26:57 +00:00
Greg Von Kuster
b75509fa17
Added tool version directories to regVariation tools directory.
2008-02-22 20:09:25 +00:00
Greg Von Kuster
218684f610
Added tool version directories for plotting tools directory.
2008-02-22 19:41:52 +00:00
Greg Von Kuster
99bc8db3fd
Added tool version directories to new_operations tools directory.
2008-02-22 19:23:18 +00:00
Greg Von Kuster
c2f5849504
Added tool version directories for metag_tools directory.
2008-02-22 18:44:05 +00:00
Greg Von Kuster
a2f475b55a
Added tool version directories for maf tool directory.
2008-02-22 18:35:01 +00:00
Greg Von Kuster
073d392616
Added tool version directories for hyphy tools, also added galaxy/tools/util directory to house utility code used acroos multiple tools.
2008-02-22 16:50:12 +00:00
Greg Von Kuster
b8599b819f
Finished adding tool version directories to filters tool directory.
2008-02-22 15:48:05 +00:00
Greg Von Kuster
32b40a5f27
Added more tool version directories for filters tool directoy.
2008-02-22 15:23:46 +00:00
Greg Von Kuster
37eeb64f61
Added tool version directory hierarchy for some tools in the filters tool directory.
2008-02-22 14:57:00 +00:00
Greg Von Kuster
dc554f04fa
Added tool version directory hierarchy for fasta_tools tool directory.
2008-02-22 14:31:30 +00:00
Greg Von Kuster
cabde35b99
Added tool version directory hierarchy for encode and extract tool directories.
2008-02-22 14:18:41 +00:00
Guruprasad Anada
82760a4c4b
Modified Lift-Over tool. The "TO" build-list will now be dynamically generated based on the input dataset's build.
2008-02-06 19:17:02 +00:00
Wen-Yu Chung
f077afa436
update several xml files for better help descriptions.
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modify section names and ids in tool_conf.xml.sample:
Fasta Tools -> FASTA manipulation
Metagenomics -> Short Read Analysis
remove short_reads_figure_length from tool_conf.xml.sample.
2008-02-05 18:32:42 +00:00
Greg Von Kuster
d28623f203
Enabling EMBOSS 5.0.0 tools, cleaned up tool_conf.xml.sample and tool_conf.xml.main.
2008-01-29 18:45:21 +00:00
Greg Von Kuster
32ccd3570c
Fixes for tabular_to_fasta and fasta_to_tabular tools - requires update to datatype_converters_conf.xml
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- Use ColumnListParameter rather than TextToolParameter
- Use better naming convertions for code and test-data files
- Added fasta_to_tabular converter to datatype_converters_conf.xml
- Fixed tool-conf so the converters are displayed in the Converters tool section
- Other miscellaneous cleanup.
2008-01-28 21:25:33 +00:00
Wen-Yu Chung
db325162ca
add version to the extract genomic dna tool.
2008-01-24 21:02:53 +00:00
Wen-Yu Chung
a33e647f11
add a section and tools for manipulating fasta file:
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convert file between fasta and tab format (should this be in section Convert Formats?);
filter fasta sequences by length;
compute lengths of fasta sequences.
add a megablast_wrapper, no functional test yet (maybe after we have designated machine?).
update extract_genomic_dna tool.
update tool_conf.xml.sample.
2008-01-22 16:45:35 +00:00
Wen-Yu Chung
45d34cc7b3
Update tools in metagenomics.
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Add one tool that deals with nib and 2bit file formats.
2008-01-21 17:49:54 +00:00
Wen-Yu Chung
7cb1467859
remove 2 tools that didn't pass functional test.
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will update later.
2008-01-18 15:20:38 +00:00
Guruprasad Anada
987e2c7c4e
Adding liftOver tool. Test section is commented as the functinal test module doesn't handle multiple outputs yet. I've downloaded liftOver mapping files from UCSC for all the genomes for which we have sequences. I've added a function in get_ucsc_scores.pl file (which contains functions to fetch sequences and alignments) to fetch liftOver mappings too.
2008-01-17 19:24:34 +00:00
Wen-Yu Chung
bd429b745e
forgot to update tool_conf.
2008-01-17 16:37:59 +00:00
Daniel Blankenberg
5b1552ffa8
Fix memory issues when dealing with MAF tools.
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Add new bx-python eggs.
Reorganize all MAF tools into a unified directory, and update tool_conf.
Remember to update tool_conf.xml from one of the samples (tool_conf.xml.sample or tool_conf.xml.main).
2008-01-16 18:01:09 +00:00
Wen-Yu Chung
9f0f822deb
add a section: metagenomics
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tools for running phred(need to change path later), trim sequence, generate boxplot and an array of length of the reads.
test data are added.
trim sequence and array of length passed functional test.
phred (2 ouput files) and boxplot (pdf file) didn't pass functional test yet.
2008-01-09 20:41:59 +00:00
Chinmay Rao
e59df6cff4
Config files reflecting updates of EMBOSS tools to v5.0
2007-12-17 17:01:23 +00:00
Guruprasad Anada
ab85984841
Adding tool "Get Indel rates for 3-way alignments" under Regional variation section.
2007-11-28 18:56:13 +00:00
Greg Von Kuster