Jeremy Goecks
b2ca2855b9
Better error message when bias correction/sequence data cannot be used in Cufflinks/compare/merge/diff.
2012-02-14 12:27:47 -05:00
Jeremy Goecks
f8f5aabb4d
Merge
2012-02-10 09:52:14 -05:00
Jeremy Goecks
18c24dade3
Tophat wrapper modifications: (a) remove parameter junctions_filter and (b) change default value of max_multihits to 20.
2012-02-10 09:23:33 -05:00
Ross Lazarus
b4d4cf0f14
Updates to FastQC wrapper
...
1) improvement suggested by bwlang to pass the history file name in as the file name to fastqc so it appears in the outputs instead of the previously unhelpful internal galaxy filename
2) lack of html output from fastqc or return of non-zero error code now triggers job failure - outputs may still be there but at least it goes red.
2012-02-10 10:40:00 +11:00
Jeremy Goecks
5cafc0b7d3
Remove maximum value for Tophat parameter initial_read_mismatches.
2012-02-08 22:56:50 -05:00
Jeremy Goecks
89072cd220
Update default values for Cufflinks' parameters.
2012-02-06 09:29:48 -05:00
John Chilton
d6ec2f021c
Specify meme requirement for fimo tool.
2012-02-02 21:29:30 -06:00
Daniel Blankenberg
c87f46ba1a
Minor cleanup for FreeBayes tool.
2012-02-02 11:14:00 -05:00
Daniel Blankenberg
c46f19051a
FreeBayes: make trace and failed alleles outputs optional.
2012-02-02 11:05:05 -05:00
Jeremy Goecks
44dbfa2c88
Update version support information in Cuff* wrappers.
2012-02-02 10:03:02 -05:00
Jeremy Goecks
7cf5495c28
Add num_threads parameter to cuffmerge wrapper script.
2012-02-02 09:26:01 -05:00
Jeremy Goecks
64d8799f59
Add num-threads param to cuffdiff.
2012-02-02 09:15:19 -05:00
Jeremy Goecks
693bc85d60
Add cuffmerge tool wrapper and functional test.
2012-02-01 22:36:17 -05:00
Daniel Blankenberg
043c0f39cf
Add a new complete FreeBayes tool configuration.
2012-02-01 11:25:18 -05:00
Daniel Blankenberg
a25dbe5603
GATK: add newly introduced gatkreport datatype, currently used by variant eval.
2012-01-27 10:46:58 -05:00
Daniel Blankenberg
43ef9becaf
Update tool test for GATK Print Reads.
2012-01-26 11:16:30 -05:00
Daniel Blankenberg
5b8845fae6
Make additional files output by SamToFastq when using read groups be fastqsanger format instead of just fastq.
2012-01-25 12:11:27 -05:00
Daniel Blankenberg
bb8309e4d4
Add sort tag to Print Reads test output element.
2012-01-25 08:54:16 -05:00
Daniel Blankenberg
718782e103
Add GATK Print Reads walker tool.
2012-01-24 16:29:28 -05:00
Daniel Blankenberg
c74f916ec0
Enhance Picard SamToFastq to allow read group aware processing.
2012-01-24 15:03:35 -05:00
Daniel Blankenberg
314fa69f71
Update GATK to version 1.4.
2012-01-23 18:03:15 -05:00
Jeremy Goecks
89128ebaa4
Better error reporting in Cufflinks.
2012-01-23 17:40:36 -05:00
Nate Coraor
40e980ab1d
Merged in jmchilton/umn-galaxy-central (pull request #28 )
2012-01-23 14:44:50 -05:00
Nate Coraor
c4a6c157b6
Merged in lance_parsons/galaxy-central-princeton (pull request #7 )
2012-01-23 14:20:37 -05:00
Daniel Blankenberg
a7c62d8159
GATK Updates.
2012-01-23 11:37:49 -05:00
Jeremy Goecks
816cbd7bf4
Remove unneeded ftype attribute.
2012-01-22 14:39:19 -05:00
Jeremy Goecks
7f94c0af21
Update cuffdiff test data for v1.3.0
2012-01-22 14:35:13 -05:00
Jeremy Goecks
39fea42347
Update test data for cufflinks v1.3.0
2012-01-22 14:06:18 -05:00
Daniel Blankenberg
ac5744c4d4
Add GATK VariantSelect tool.
2012-01-19 16:16:31 -05:00
Ross Lazarus
3a11a5893f
Fixed composite download zip file failure related to trying to delete a file whose file handle was needed as the return value
...
Added an option to show column header names in check box style select lists so to minimise errors trying to remember or look them up
Added more information on the required format for PicardHsMetrics bait/target files
2012-01-19 12:01:20 +11:00
Nate Coraor
e17c256d52
Merge galaxy-central.
2012-01-18 14:34:27 -05:00
Nate Coraor
c362e6202e
A bit more actual user cleaning.
2012-01-18 14:34:00 -05:00
Nate Coraor
61062a3ae5
Merge galaxy-central.
2012-01-18 10:34:39 -05:00
Daniel Blankenberg
60d477cea5
Have GOPs Concatenate tool always respect the provided strand column.
2012-01-18 10:30:08 -05:00
Jeremy Goecks
86bc8cab3e
Update Tophat tests for v1.4.0
2012-01-18 09:48:32 -05:00
Daniel Blankenberg
8d7f1917f5
Better handling of JEXL expressions in GATK.
2012-01-17 15:28:00 -05:00
Daniel Blankenberg
6f6f815a9c
Better handling of JexlExpressions in stratification expressions for GATK VariantEval.
2012-01-11 08:33:48 -05:00
Daniel Blankenberg
5d9db8b334
GATK variant eval Update.
2012-01-10 14:15:18 -05:00
Jeremy Goecks
2d5b74aa6d
Set Cufflinks global model when upper quartile normalization is used.
2011-12-22 13:54:33 -05:00
Lance Parsons
5bbb432cd8
Removed uneccessary hide_stderr.py script from samtools
2011-12-22 11:16:28 -05:00
Lance Parsons
98cdf4c33e
Merged sam_merge fixes from galaxy-central keeping change to set TMP_DIR
2011-12-22 11:13:07 -05:00
Jeremy Goecks
cdab8a7804
Trackster: add support for including a global model when running tools in Trackster. This is done by using a new HiddenDataToolParameter and implementing 'set parameter' actions in a tool's trackster configuration. Cufflinks now uses a global model to produce correct output when run in Trackster.
2011-12-21 17:04:23 -05:00
Dave Clements
9d0e631203
Updated "Example" images shown at the bottom of many
...
"Operate on Genomic Invervals" tool pages. Old onew were looking dated.
New ones look, well, newer, and cover more cases.
2011-12-19 02:44:31 -08:00
Daniel Blankenberg
d59b7ec591
Add Maximal Information-based Nonparametric Exploration (MINE) tool.
2011-12-16 12:54:21 -05:00
Daniel Blankenberg
99c7409900
Update EBI SRA tool's input action.
2011-12-14 09:37:45 -05:00
Daniel Blankenberg
2351c4aaca
Add EBI ENA SRA tool contributed by Iain Cleland.
2011-12-13 09:45:49 -05:00
Nate Coraor
85ba013e6d
Actual User: Fix for newline conversion on upload, tighten file permissions for files in upload. Please make sure you clean your temp directory regularly.
2011-12-08 13:22:39 -05:00
Daniel Blankenberg
7d4b23e1d9
Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610 .
2011-12-08 10:44:42 -05:00
Nate Coraor
03c4fa3689
The upload tool requires samtools to upload BAM files, the Pileup tool requires samtools <= 0.1.16.
2011-12-06 11:42:12 -05:00
Daniel Blankenberg
5078b6ea58
Update GATK tools handling annotations to allow manually specifying additional annotation names to apply.
2011-12-06 09:42:56 -05:00
Jeremy Goecks