Jeremy Goecks 5775716a03 Merged in chapmanb/galaxy-central-apiupload (pull request #74)

2012-10-08 22:44:02 -05:00

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annotation_profiler

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data_destination

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data_source

Correctly set history and handle output datasets for error cases in tool API. Allow specification of dataset name during uploads, exposing through API

2012-10-04 15:31:16 -04:00

discreteWavelet

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

encode

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evolution

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -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

Fix for fastq filter tests of paired_end boolean.

2012-09-14 15:50:38 -04:00

fastx_toolkit

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

filters

Add feature/attribute name indexing framework to converters. Provide full text indexing for GFF attributes.

2012-08-16 16:32:00 -04:00

gatk

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

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

genetrack

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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

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indels

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maf

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

meme

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metag_tools

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

multivariate_stats

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mutation

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

new_operations

fix to mako import and some up-stack error reporting in tools

2012-08-08 12:30:25 -04:00

next_gen_conversion

Fixed error in solid2fasta.xml preventing help text from displaying.

2012-09-04 10:15:18 -04:00

ngs_rna

Cuffcompare wrapper: only include refmap datasets if reference annotation is used.

2012-09-27 14:12:15 -04:00

ngs_simulation

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

peak_calling

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phenotype_association

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -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

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

regVariation

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

rgenetics

More JS file reorganization: (a) move IE and rgenetics into their own directories; (b) move additional external libraries to libs.

2012-08-21 16:54:19 -04:00

samtools

Require pileup format as input to pileup parser tool.

2012-08-23 15:58:11 -04:00

solid_tools

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

sr_assembly

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sr_mapping

Remove the bwa wrappers from the repository.

2012-10-01 09:24:33 -04:00

stats

Add logical operators to the compute tool whitelist.

2012-10-08 10:28:29 -04:00

taxonomy

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

validation

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vcf_tools

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visualization

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