Jeremy Goecks 0c00e50a54 Move implementation of from_work_dir attribute from job finish to job command line so that outputs are available earlier. This provides compatibility of attribute when setting metadata externally. Update Tophat wrapper to act as exemplar for attribute use.

2012-07-20 13:18:54 -04:00

..

annotation_profiler

Add information for UCSC data to annotation profiler.

2011-11-16 10:40:55 -05:00

data_destination

merging from central

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

data_source

Rewrite HbVar datasource tool.

2012-05-04 15:35:51 -04:00

discreteWavelet

Update for wavelet variance tool contributed by Erika Kvikstad.

2011-08-30 09:33:10 -04:00

encode

Tool help updates.

2011-09-21 04:11:07 -04:00

evolution

changes to aaChanges interface

2012-04-02 14:28:08 -04:00

extract

Clean up temp files.

2012-03-09 16:11:21 -05:00

fasta_tools

Enable fasta_to_len conversion to use only first word in title; this is standards compliant and used by default for automatic conversion.

2012-03-08 11:09:14 -05:00

fastq

Update FASTQ Groomer tool help to indicate that Illumina 1.8+ is Sanger encoded.

2011-11-08 16:53:19 -05:00

fastx_toolkit

Minor tool help updates.

2011-09-08 10:34:56 -04:00

filters

Full and proper sorting for GTF datasets: sort by, in order, transcript_id, chrom, and start.

2012-05-24 13:26:48 -04:00

gatk

Add argument names to parameter help for GATK tools' options.

2012-04-10 16:22:45 -04:00

genetrack

Update GeneTrack help.

2011-11-10 11:54:50 -05:00

genomespace

Update GenomeSpace exporter tool to use the newly introduced /personaldirectory as the root for auto-generated export paths.

2012-05-04 14:31:22 -04:00

hyphy

Added functional test for hyphy NJ tree builder.

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

indels

Remove imports of the sets module, set has been a standard type since 2.4. There are more in tools, but they check for the existence of set() first, so will not raise a warning.

2010-09-27 21:35:03 -04:00

maf

MAF stats tool will now skip intervals with length less 1.

2011-09-23 09:36:57 -04:00

meme

Specify meme requirement for fimo tool.

2012-02-02 21:29:30 -06:00

metag_tools

Fixed number of threads

2012-04-26 16:49:38 +02:00

multivariate_stats

Fixed a bug in PCA tool - standard deviation & prop variance values are now sorted by PC order.

2011-07-15 10:33:02 -04:00

mutation

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

ncbi_blast_plus

Correct comment in NCBI BLAST+ wrappers

2012-04-13 15:07:12 +01:00

new_operations

Have GOPs Concatenate tool always respect the provided strand column.

2012-01-18 10:30:08 -05:00

next_gen_conversion

Update links to reflect Galaxy Wiki moving away from Bitbucket.

2011-07-18 18:10:55 -05:00

ngs_rna

Move implementation of from_work_dir attribute from job finish to job command line so that outputs are available earlier. This provides compatibility of attribute when setting metadata externally. Update Tophat wrapper to act as exemplar for attribute use.

2012-07-20 13:18:54 -04:00

ngs_simulation

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

peak_calling

Tool help updates.

2011-11-14 13:26:29 -05:00

phenotype_association

Add FreeBayes to tool_conf.xml.main.

2012-03-27 18:09:55 -04:00

picard

Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py

2012-04-05 02:16:12 +10:00

plotting

Minor tool help updates.

2011-09-08 10:34:56 -04:00

regVariation

Suppressed R package-loading messages which were previously being written into stderr

2012-05-25 10:54:03 -04:00

rgenetics

Add some more missing quotes to command line.

2012-06-08 08:28:35 +10:00

samtools

Fix typo in BAM slice tool.

2012-05-02 11:47:04 -04:00

solid_tools

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

sr_assembly

Velvet wrapper: fix typos, tabs -> spaces, spacing

2011-05-27 11:01:46 +02:00

sr_mapping

Have Bowtie2 wrapper produce BAM rather than SAM output.

2012-06-11 15:52:36 -04:00

stats

Add Maximal Information-based Nonparametric Exploration (MINE) tool.

2011-12-16 12:54:21 -05:00

taxonomy

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

validation

…

vcf_tools

Fix for vcf_extract tool test

2011-03-02 09:40:10 -05:00

visualization

Minor tool help updates.

2011-09-08 10:34:56 -04:00