 Jeremy Goecks
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0c12da85ba
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Add min, max insert size parameters to bowtie2 wrapper.
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2012-06-08 14:03:41 -04:00 |
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Jeremy Goecks
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a08c0c03ce
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Fix bug in setting Bowtie2 parameters.
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2012-06-08 13:48:37 -04:00 |
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Ross Lazarus
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c14fcf5ea0
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Add some more missing quotes to command line.
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2012-06-08 08:28:35 +10:00 |
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Ross Lazarus
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9fbf7007c7
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Updates to fastqc tool to wrap the user supplied job name in quotes and sanitize to letters/digits only
Some downstream problems from ( characters reported today but probably needs deeper sanitizing
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2012-06-08 08:26:09 +10:00 |
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Jeremy Goecks
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63fec8c332
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Add preset alignment options to Bowtie2 wrapper and fix default in Tophat2 wrapper.
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2012-06-06 15:27:59 -04:00 |
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Jeremy Goecks
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d802171ccb
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Update default and help for Tophat2 coverage search parameter.
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2012-06-06 14:42:21 -04:00 |
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Jeremy Goecks
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f7cfc540bd
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Clarify inputs for forward, reverse reads in Tophat2 wrapper.
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2012-06-04 09:29:51 -04:00 |
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Jeremy Goecks
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51312405f4
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Add Bowtie2 preset options to Tophat2 wrapper.
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2012-05-31 11:08:24 -04:00 |
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Jeremy Goecks
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2b023cc95f
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Tophat2 wrapper updates: (a) use bowtie2-build; (b) add option to report discordant pairs; (c) update tests.
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2012-05-31 10:08:13 -04:00 |
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Jeremy Goecks
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27f7aa9fde
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Clearer explanation and help for default vs. full parameter settings.
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2012-05-30 19:47:40 -04:00 |
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Guruprasad Anada
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1d6a796f94
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Suppressed R package-loading messages which were previously being written into stderr
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2012-05-25 10:54:03 -04:00 |
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Jeremy Goecks
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df28aec040
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Full and proper sorting for GTF datasets: sort by, in order, transcript_id, chrom, and start.
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2012-05-24 13:26:48 -04:00 |
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Jeremy Goecks
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35373ec78f
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Merged in jmchilton/umn-galaxy-central/add_weblogo_requirement (pull request #33)
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2012-05-23 22:39:40 -04:00 |
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Jeremy Goecks
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4318998692
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Merged in jmchilton/umn-galaxy-central/add_clustalw2_requirement (pull request #34)
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2012-05-23 22:39:00 -04:00 |
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Daniel Blankenberg
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89e347625f
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Rewrite HbVar datasource tool.
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2012-05-04 15:35:51 -04:00 |
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Daniel Blankenberg
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14734e345a
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Update GenomeSpace exporter tool to use the newly introduced /personaldirectory as the root for auto-generated export paths.
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2012-05-04 14:31:22 -04:00 |
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Daniel Blankenberg
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26e75b3e60
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Allow GenomeSpace importer tool to sniff filetype when GSMetadata object is not available.
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2012-05-03 12:25:06 -04:00 |
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Daniel Blankenberg
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c44aee110d
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Update WormBase datasource tool to use WormBase 2.
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2012-05-02 17:04:33 -04:00 |
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Daniel Blankenberg
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24e9b5df93
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Fix typo in BAM slice tool.
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2012-05-02 11:47:04 -04:00 |
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Daniel Blankenberg
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e8fe4c4dc1
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Add Slice BAM by regions tool.
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2012-05-02 11:32:19 -04:00 |
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Jeremy Goecks
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0cb9ceee2a
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Revert Tophat wrapper version #.
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2012-04-30 11:46:43 -04:00 |
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Jeremy Goecks
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f64f71e7ff
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Revert Tophat wrapper due to parameter incompatibility issues.
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2012-04-30 11:41:04 -04:00 |
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Jeremy Goecks
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9c7e7d8635
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Merge
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2012-04-29 20:34:39 -04:00 |
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Jeremy Goecks
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633c3cb9d5
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Update Cuffdiff min-alignment-count default.
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2012-04-28 22:21:30 -04:00 |
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Jeremy Goecks
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80f70cd0de
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More cleaning of Tophat wrapper.
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2012-04-27 15:22:11 -04:00 |
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Jeremy Goecks
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7c40df458e
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Skeleton wrapper for Bowtie2.
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2012-04-26 15:28:17 -04:00 |
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Jeremy Goecks
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78ce10ae5f
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Remove version code from tophat wrappers as this is now handled by <version> tag.
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2012-04-26 14:25:01 -04:00 |
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Jeremy Goecks
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5ad68c65d3
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Fix version references in tophat2 wrapper.
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2012-04-26 13:59:03 -04:00 |
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Anton Nekrutenko
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8cda02d849
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Fixed number of threads
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2012-04-26 16:49:38 +02:00 |
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Anton Nekrutenko
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a2eb104b31
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Modified metagenomic mapper to use BLAST+ blastn in megablast mode
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2012-04-26 16:44:26 +02:00 |
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Jeremy Goecks
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ccb1b9f112
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Revert Tophat wrapper to support versions 1.3.0-1.4.1
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2012-04-25 11:33:05 -04:00 |
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Jeremy Goecks
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64d1faeeb2
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Add explicit Tophat2 wrapper.
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2012-04-25 11:25:17 -04:00 |
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Jeremy Goecks
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1747527142
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Include more Tophat2 options.
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2012-04-24 22:30:22 -04:00 |
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Jeremy Goecks
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f4350d5712
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Add fusion search parameters to Tophat wrapper.
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2012-04-24 10:35:27 -04:00 |
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Jeremy Goecks
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e2ea763bcb
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Update Trinity wrapper to support most recent versions.
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2012-04-23 15:29:37 -04:00 |
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Jeremy Goecks
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82fbebe842
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Refactor and simply tophat wrapper.
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2012-04-22 11:58:24 -04:00 |
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Jeremy Goecks
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7535ec1326
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Basic support for Tophat2.
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2012-04-20 17:08:55 -04:00 |
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Daniel Blankenberg
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8163333bdb
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Slightly more unique automatically generated filename for GenomeSpace export.
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2012-04-18 19:38:34 -04:00 |
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Jeremy Goecks
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26070bd162
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Tophat wrapper: (a) add documentation for versions supported and (b) always return insertions and deletetions outputs.
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2012-04-18 09:23:33 -04:00 |
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Peter Cock
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6c2076e879
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Correct comment in NCBI BLAST+ wrappers
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2012-04-13 15:07:12 +01:00 |
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Daniel Blankenberg
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2d5b8eca2f
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Add argument names to parameter help for GATK tools' options.
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2012-04-10 16:22:45 -04:00 |
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Daniel Blankenberg
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d38b177307
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Fix inconsequential warning about when tag when loading FreeBayes.
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2012-04-10 16:08:15 -04:00 |
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Daniel Blankenberg
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5bcce30d58
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Fix inconsequential warning about when tag when loading samtools mpileup.
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2012-04-10 16:07:19 -04:00 |
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Daniel Blankenberg
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7de86f1fb6
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Update argument names to parameter help for GATK Advanced options.
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2012-04-10 11:46:46 -04:00 |
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Daniel Blankenberg
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62506054cd
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Add argument names to parameter help for GATK Advanced options.
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2012-04-10 11:20:12 -04:00 |
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Daniel Blankenberg
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0372d1fe06
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Fix for BWA -R option.
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2012-04-10 09:24:25 -04:00 |
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Nate Coraor
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cc2385220f
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Miller Lab's Genome Diversity tools moved to the Tool Shed.
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2012-04-09 13:13:44 -04:00 |
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Ross Lazarus
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8a9c206a5b
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Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py
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2012-04-05 02:16:12 +10:00 |
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Ross Lazarus
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1deefe54c2
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Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space.
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2012-04-04 07:56:46 +10:00 |
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Ross Lazarus
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f71f0ff9d2
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Patch for picard_AddOrReplaceReadGroups.xml to add --tmpdir "${__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.
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2012-04-04 06:11:54 +10:00 |
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