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.' ...

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

..

annotation_profiler

Resync Annotation Profiler tests to current cached data.

2010-06-02 16:40:39 -04:00

data_destination

merging from central

2008-10-28 11:28:15 -04:00

data_source

Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.

2010-08-19 13:58:10 -04:00

discreteWavelet

Adding wavelet analysis tools made by Zaky from Makova lab.

2010-08-16 18:30:37 -04:00

emboss_5

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.

2009-12-07 10:19:41 -05:00

encode

Fix gencode partition tool to not use hard-coded paths.

2009-12-09 15:21:41 -05:00

evolution

Next rev of codingSnps tool.

2010-03-24 14:14:58 -04:00

extract

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.'

2010-08-26 12:00:41 -04:00

fasta_tools

Sync hashbangs

2010-04-01 20:36:31 -04:00

fastq

Enhance Tool Repeat Grouping parameter to allow specifying min, max, and default repeat unit counts.

2010-07-14 12:15:14 -04:00

fastx_toolkit

Fix accidentally committed fastx tool configs

2010-01-07 16:20:04 -05:00

filters

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.'

2010-08-26 12:00:41 -04:00

genetrack

Add bed6 and bed12 datatypes, which are subclasses of bedstrict; converters are available to turn any interval datatype into these types. Change GeneTrack Indexer tool and converter to use bed6 as input.

2010-04-01 13:08:48 -04:00

hyphy

Added functional test for hyphy NJ tree builder.

2010-02-04 11:56:58 -05:00

indels

Updated indel analysis tools: fixed counting bugs in indel_analysis and improved help section; standardized CIGAR regex across tools; updated test files for several tools

2010-07-21 16:25:46 -04:00

maf

Automated merge with https://bitbucket.org/galaxy/galaxy-central/

2010-08-04 14:01:39 -04:00

metag_tools

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

multivariate_stats

Fixed functional tests for kcca, linear regression and get indels tools. Have used 're_match' to accommodate sign and decimal precision changes in kcca output.

2010-06-09 12:52:47 -04:00

mutation

Bug fixes and basic zoom feature for mutation viz tool

2010-08-25 16:47:39 -04:00

new_operations

Fixed another bug in column join so it will handle filling empty columns properly

2010-08-20 17:04:16 -04:00

next_gen_conversion

Updated output format for solid2fastq converter

2010-04-07 08:44:57 -04:00

ngs_rna

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.'

2010-08-26 12:00:41 -04:00

peak_calling

Add eland and elandmulti formats. Enhance MACs peakcaller to properly handle these formats.

2010-04-27 10:59:46 -04:00

plotting

Make boxplot tool respect exit codes when determining job errors: makes e.g. 'Could not find/open font when opening font "arial", using internal non-scalable font' a non-fatal warning. Add version attribute to gnuplot requirement tag.

2010-03-22 11:06:40 -04:00

regVariation

Don't pipe errors for compute_q_values to a file so we can find out what the error is

2010-08-19 17:03:54 -04:00

rgenetics

Fixes for rgManQQ - manhattan and qqplot generator for

2010-07-15 04:58:08 -04:00

samtools

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

solid_tools

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

sr_assembly

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

sr_mapping

Fixing buildbot tests: added missing column join test files; regenerated and enhanced BWA test files; sorted tophat_out1.sam and specified sort=True in test for it

2010-08-25 21:51:41 -04:00

stats

Modified Group tool by adding Mode function to the list of aggregate operations.

2010-07-29 12:21:09 -04:00

taxonomy

Bug fixes to LCA tool

2010-02-22 16:22:12 -05:00

validation

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

visualization

Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.

2010-02-05 16:06:27 -05:00