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1917 Commits
Author SHA1 Message Date
Daniel Blankenberg 89e347625f Rewrite HbVar datasource tool. 2012-05-04 15:35:51 -04:00
Daniel Blankenberg 14734e345a 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
Daniel Blankenberg 26e75b3e60 Allow GenomeSpace importer tool to sniff filetype when GSMetadata object is not available. 2012-05-03 12:25:06 -04:00
Daniel Blankenberg c44aee110d Update WormBase datasource tool to use WormBase 2. 2012-05-02 17:04:33 -04:00
Daniel Blankenberg 24e9b5df93 Fix typo in BAM slice tool. 2012-05-02 11:47:04 -04:00
Daniel Blankenberg e8fe4c4dc1 Add Slice BAM by regions tool. 2012-05-02 11:32:19 -04:00
Jeremy Goecks 0cb9ceee2a Revert Tophat wrapper version #. 2012-04-30 11:46:43 -04:00
Jeremy Goecks f64f71e7ff Revert Tophat wrapper due to parameter incompatibility issues. 2012-04-30 11:41:04 -04:00
Jeremy Goecks 9c7e7d8635 Merge 2012-04-29 20:34:39 -04:00
Jeremy Goecks 633c3cb9d5 Update Cuffdiff min-alignment-count default. 2012-04-28 22:21:30 -04:00
Jeremy Goecks 80f70cd0de More cleaning of Tophat wrapper. 2012-04-27 15:22:11 -04:00
Jeremy Goecks 7c40df458e Skeleton wrapper for Bowtie2. 2012-04-26 15:28:17 -04:00
Jeremy Goecks 78ce10ae5f Remove version code from tophat wrappers as this is now handled by <version> tag. 2012-04-26 14:25:01 -04:00
Jeremy Goecks 5ad68c65d3 Fix version references in tophat2 wrapper. 2012-04-26 13:59:03 -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
Jeremy Goecks ccb1b9f112 Revert Tophat wrapper to support versions 1.3.0-1.4.1 2012-04-25 11:33:05 -04:00
Jeremy Goecks 64d1faeeb2 Add explicit Tophat2 wrapper. 2012-04-25 11:25:17 -04:00
Jeremy Goecks 1747527142 Include more Tophat2 options. 2012-04-24 22:30:22 -04:00
Jeremy Goecks f4350d5712 Add fusion search parameters to Tophat wrapper. 2012-04-24 10:35:27 -04:00
Jeremy Goecks e2ea763bcb Update Trinity wrapper to support most recent versions. 2012-04-23 15:29:37 -04:00
Jeremy Goecks 82fbebe842 Refactor and simply tophat wrapper. 2012-04-22 11:58:24 -04:00
Jeremy Goecks 7535ec1326 Basic support for Tophat2. 2012-04-20 17:08:55 -04:00
Daniel Blankenberg 8163333bdb Slightly more unique automatically generated filename for GenomeSpace export. 2012-04-18 19:38:34 -04:00
Jeremy Goecks 26070bd162 Tophat wrapper: (a) add documentation for versions supported and (b) always return insertions and deletetions outputs. 2012-04-18 09:23:33 -04:00
Peter Cock 6c2076e879 Correct comment in NCBI BLAST+ wrappers 2012-04-13 15:07:12 +01:00
Daniel Blankenberg 2d5b8eca2f Add argument names to parameter help for GATK tools' options. 2012-04-10 16:22:45 -04:00
Daniel Blankenberg d38b177307 Fix inconsequential warning about when tag when loading FreeBayes. 2012-04-10 16:08:15 -04:00
Daniel Blankenberg 5bcce30d58 Fix inconsequential warning about when tag when loading samtools mpileup. 2012-04-10 16:07:19 -04:00
Daniel Blankenberg 7de86f1fb6 Update argument names to parameter help for GATK Advanced options. 2012-04-10 11:46:46 -04:00
Daniel Blankenberg 62506054cd Add argument names to parameter help for GATK Advanced options. 2012-04-10 11:20:12 -04:00
Daniel Blankenberg 0372d1fe06 Fix for BWA -R option. 2012-04-10 09:24:25 -04:00
Nate Coraor cc2385220f Miller Lab's Genome Diversity tools moved to the Tool Shed. 2012-04-09 13:13:44 -04:00
Ross Lazarus 8a9c206a5b 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
Ross Lazarus 1deefe54c2 Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space. 2012-04-04 07:56:46 +10:00
Ross Lazarus f71f0ff9d2 Patch for picard_AddOrReplaceReadGroups.xml to add --tmpdir "${__new_file_path__}" to the command line generated. That will over-ride the default value "/tmp" for opts.tmpdir in picard_wrapper.py and solve the problem with /tmp filling reported by Matt Shirley. 2012-04-04 06:11:54 +10:00
Richard Burhans c3765659ea changes to aaChanges interface 2012-04-02 14:28:08 -04:00
Daniel Blankenberg 4bc632aaa8 Fix for --multiallelic in Unified Genotyper. 2012-04-02 10:09:00 -04:00
Daniel Blankenberg 9894c0bd9a Small fix for setting upload path in GenomeSpace export tool. 2012-03-30 17:08:35 -04:00
Daniel Blankenberg 195e08f2b1 Add GenomeSpace tools. 2012-03-29 10:24:28 -04:00
Daniel Blankenberg d72a179e6e Add FreeBayes to tool_conf.xml.main. 2012-03-27 18:09:55 -04:00
Richard Burhans 77f391c6ae changes to aaChanges tool 2012-03-22 13:19:31 -04:00
Richard Burhans ff1b05d283 Updates to Human Genome Variation tools 
Rename Human Genome Variation to Phenotype Association
 2012-03-22 13:03:01 -04:00
Greg Von Kuster d6302da05c Eliminte the emboss_5 tools. 2012-03-21 16:46:39 -04:00
Jeremy Goecks 2ebe0eb774 Clean up temp files. 2012-03-09 16:11:21 -05:00
Jeremy Goecks 047c1bff2f 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
Jeremy Goecks 12c9c98b95 Add necessary space after threads option in Cuffmerge. 2012-03-08 08:37:20 -05:00
Daniel Blankenberg 1fb7388e59 Fix for GATK Depth of coverage tool when using advanced GATK options with one or more target interval inputs defined. 2012-03-01 10:11:55 -05:00
Dannon Baker 631cb80f59 Merged in peterjc/galaxy-central/split_blast (pull request #37) 2012-02-28 12:26:29 -05:00
Daniel Blankenberg 3fbcb4bfc1 Remove bam index metadata validator from GATK tools. The GATK wrapper will now build missing bam indexes on the fly as needed. 2012-02-27 12:49:30 -05:00