Dave Bouvier
a3018feb02
Migrate 22 tools from the distribution to the tool shed.
2014-05-19 13:01:46 -04:00
Dave Bouvier
5f485f05b3
Remove tool that was migrated to the tool shed in 10719:c2f06b5cfba1. Remove test data that belonged to tools that were removed in 12288:401ee23dcf2f.
2014-02-17 13:05:00 -05:00
John Chilton
cfb194f0a0
Enhance megablast to utilize GALAXY_SLOTS configuration when available.
2013-11-05 13:46:06 -06:00
Jeremy Goecks
9a5679c37c
Use mako template in tool help so that dynamic image paths can be used. Fixes #141
2012-08-07 09:40:51 -04:00
Anton Nekrutenko
8cda02d849
Fixed number of threads
2012-04-26 16:49:38 +02:00
Anton Nekrutenko
a2eb104b31
Modified metagenomic mapper to use BLAST+ blastn in megablast mode
2012-04-26 16:44:26 +02:00
Daniel Blankenberg
023c4db69e
Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.
2011-11-29 17:30:14 -05:00
Kanwei Li
286c8f2af6
Improve BLAST parser tool error handling, and improve elementtree import as well.
2011-07-12 18:14:56 -04:00
Nate Coraor
b77ec95d0b
Fix for either a bug or undocumented feature in ElementTree that broke megablast and blast+ XML parsing in Python 2.7.
2011-06-09 11:22:23 -04:00
Kanwei Li
2d0b8eb830
Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141
2010-12-14 14:22:13 -05:00
Kelly Vincent
7d0ff14df9
Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.
2010-11-08 00:10:13 -05:00
Nate Coraor
e05f11bc73
Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'.
2010-10-07 16:23:57 -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
Kelly Vincent
eeca0c723a
Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output
2010-04-12 15:56:13 -04:00
Kanwei Li
0952b28502
Sync hashbangs
2010-04-01 20:36:31 -04:00
Kelly Vincent
38ad670389
Updated several NGS tools to better handle stderr (allow for extremely large stderr output)
2010-03-30 16:33:19 -04:00
Nate Coraor
0bfa58679b
Fix locations of cached data for tests
2010-02-25 12:27:07 -05:00
Daniel Blankenberg
8082c6f36f
Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid.
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Tools include:
FASTQ Groomer convert between various FASTQ quality formats
Combine FASTA and QUAL into FASTQ
FASTQ joiner on paired end reads
FASTQ splitter on joined paired end reads
FASTQ to FASTA converter
FASTQ Summary Statistics by column
Filter FASTQ reads by quality score and length
FASTQ Trimmer by column
Manipulate FASTQ reads on various attributes
Boxplot of quality statistics (Generic, with outliers)
2010-02-23 16:48:07 -05:00
Greg Von Kuster
927cfe685c
Fixed my previous fix for copying history items to a library, which really didn't fix anything.  Fixed the functional tests for lav_to_bed, split_paired_reads, and solid2fastq by adding the 2nd output dataset to the test for each tool.  Renamed the test files for the tools to have the Galaxy supported file extension.
2010-01-14 09:44:58 -05:00
Guruprasad Anada
fb9147e83d
Fixed functional tests for short_reads_figure_score tool.
2010-01-08 11:28:37 -05:00
Nate Coraor
49a0fcc92f
fix for parsing blastdb.loc for the megablast wrapper tool
2009-12-15 19:18:22 -05:00
Greg Von Kuster
aa36d79d30
Update the output datasets for functional test for the quality_score_distribution tool due to a new version of R - update tool version as well.
2009-12-10 10:56:01 -05:00
Kelly Vincent
ebc67a6bc7
Updated megablast_wrapper tool to allow for date to be included with database name and displayed (so user knows how current it is)
2009-12-09 18:50:12 -05:00
Nate Coraor
56032de2bd
Upgrade to Cheetah 2.2.2
2009-11-10 13:47:34 -05:00
Kelly Vincent
03cb53ead3
Fixed megablast_wrapper test to use phiX database and modified parameter passing to use named parameters
2009-11-10 13:06:20 -05:00
Anton Nekrutenko
854fb020b8
Modified test data and tool conf for fastq stats
2009-10-08 14:50:28 -04:00
Anton Nekrutenko
809f774f36
ngs updates
2009-10-07 11:18:14 -04:00
Kanwei Li
3531212ff6
typo fixes for tools in folders A-M
2009-09-27 23:11:43 -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
2105021def
small tweaks
2009-09-18 11:11:41 -04:00
Anton Nekrutenko
c4b8764d6f
Modification for input datatype in the splitter:w
2009-09-15 10:30:54 -04:00
Anton Nekrutenko
28ccd18f7d
Modifications for fastq splitted help
2009-09-14 15:27:55 -04:00
Anton Nekrutenko
bf9666bf21
Fixed a stupid and truly horrible paired end splitter bug
2009-08-20 17:33:39 -04:00
Daniel Blankenberg
da67dccfda
Fix megablast wrapper never cleaning up tempfiles.
2009-08-03 16:23:37 -04:00
Guruprasad Anada
ee3cddc5df
Replacing \"qual\" datatype with 3 new datatypes: qualsolid, qual454 and qualsolexa.
2009-04-29 11:53:22 -04:00
Anton Nekrutenko
871dfe4a6d
Added column info to MB wrapper
2009-04-24 15:06:51 -04:00
Anton Nekrutenko
309204e5f9
Fixed finf_diag_hits plus a ttypo correction
2009-04-21 09:36:42 -04:00
Greg Von Kuster
86c7a80c31
Add support for NCBI Blast XML data format.
2009-01-07 12:20:35 -05:00
Nate Coraor
d337613eeb
megablast fix from Anton
2009-01-05 15:26:17 -05:00
Wen-Yu Chung
b31191d4bd
fix for short read score distribution tool. restore test data.
2008-12-19 14:25:43 -05:00
Wen-Yu Chung
170f9d2d77
fixed for short read build distribution tool. remove unused arrays. also update test data output.
2008-12-19 12:25:52 -05:00
Wen-Yu Chung
b3bcbdcf15
update xml files for short reads mapping tools.
2008-10-15 15:51:13 -04:00
Wen-Yu Chung
0021c40c85
add shrimp_color_space mapping tool with functional test data.
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add a new datatype called csfasta.
2008-10-13 15:06:42 -04:00
Wen-Yu Chung
d7b7c0795f
add error msg for shrimp_wrapper when memory error and zero hits.
...
convert last column of megablast output to float.
2008-09-30 16:40:42 -04:00
Wen-Yu Chung
07118387a1
Fix a bug in shrimp_wrapper and add a tool for splitting paired-end reads.
...
Update datatype/fastqsolexa so the number of sequences is correct.
2008-09-19 12:02:13 -04:00
Wen-Yu Chung
5adbb0ef6f
update shrimp_wrapper.
2008-09-18 15:41:23 -04:00
Guruprasad Anada
fd8458e86a
New tool to format short read mapping data as a UCSC custom track,.
2008-09-17 16:42:08 -04:00
Wen-Yu Chung
bca6ad57e1
add SHRiMP mapper for short reads analysis.
2008-09-15 15:04:41 -04:00
Anton Nekrutenko
74d5327978
Lastz with additional short read changes
2008-09-12 15:14:20 -04:00
Greg Von Kuster
57ac81b508
Reverting extract_genomic_dna and blat_wrapper tools to rev 1472.
2008-08-21 08:54:51 -04:00
Dave Bouvier