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243 Commits
Author SHA1 Message Date
Martin Cech 709abedcb4 Merged in anton/galaxy-central-anton (pull request #539) 
Initial tweaks to tool_conf.xml sample and one of the tools.
 2014-11-11 12:26:45 -05:00
Nicola Soranzo fbcf3e2bbc Make stripping and condensing optional. 2014-10-28 16:57:49 +01:00
Nicola Soranzo 526c2507d7 dos2unix 2014-10-28 12:21:00 +01:00
Anton Nekrutenko 873d1f455c uniq.xml edited online with Bitbucket 2014-10-23 16:42:15 +00:00
Dannon Baker 9d85ca9e23 Switch to_json_string/from_json_string in galaxy/tools. 2014-09-09 10:06:35 -04:00
Björn Grüning b9389cc76d Add empty_field validator to gtf2bedgraph.xml 2014-06-27 22:21:37 +00:00
Dannon Baker a6b6879f12 Reorder imports post-PR 403. 2014-06-09 10:53:00 -04:00
Saket Choudhary 769a1d4f49 PEP8 fixes, close find handles for 'convert delimiters to tab' tool 2014-06-09 11:56:06 +05:30
Dannon Baker 559ecb4ec8 Remove dependency on simplejson; convert everything over to using the json module in the python standard library. 2014-01-10 07:29:05 -05:00
John Chilton 53cb37aed3 Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines. 
As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html).

There are still two copies.
 2013-11-07 12:56:48 -05:00
John Chilton 73206460d6 Backed out changeset 9532e80796ec 2013-11-07 13:02:22 -05:00
John Chilton 4a3820ef58 Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines. 
As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html).

There are still two copies.
 2013-11-07 12:56:48 -05:00
Dannon Baker 63e9ba7f27 Merged in ghuls/galaxy-central/sort (pull request #172) 
Fix sorting of numbers in scientific notation.
 2013-08-07 13:33:27 -04:00
Jeremy Goecks bc27b54627 Add semicolon to the list of delimiters in the 'Convert delimiters to whitespace tool'. 2013-06-21 11:59:13 -04:00
Gert Hulselmans f0ee6b578e Fix sorting of numbers in scientific notation. 
The -n option of sort can't handle numbers in scientific notation.
The -g option of sort can handle those numbers correctly.
 2013-05-28 15:48:45 +02:00
Aysam Guerler 0e0f2605fa grep/select tool: fixed tab-delimiter matching for GNU version of grep 2013-04-02 15:18:22 -04:00
Jeremy Goecks 6a69ebc669 Merge in next-stable 2013-03-21 12:19:45 -04:00
Jeremy Goecks bacf200965 Add support for column ranges to Cut tool. Thank to John Chilton for this code. 2013-03-21 12:19:14 -04:00
Aysam Guerler 109f6c8316 tool tip fix for fastq summary and sorter 2013-03-19 11:50:03 -04:00
Aysam Guerler e26eb773aa Provide backwards compatibility for sorter 2013-03-15 17:29:29 -04:00
Aysam Guerler 8cd17848ad sort: update log to browser 2013-03-08 12:10:19 -05:00
Aysam Guerler bdbd21f250 sort: preserves comments in sorted output 2013-03-08 11:52:37 -05:00
Joachim Jacob 3dd11e95d8 Adjusted trimming tool to include negative positions. Modified help and test. 2013-01-30 10:38:58 +01:00
Jeremy Goecks 9719bed6f9 Enable BedGraph to be used as input to wig-to-bigwig tool. 2013-01-24 17:06:51 -05:00
Dave Clements f706f34948 Replaced "query" with "dataset" in a number of tool definition XML files. 
I got tired of coming across "query" when doing workshops.
 2013-01-14 16:13:54 -08:00
Jeremy Goecks e23d56219b Fix output definition for GTF filter by attribute values list/ 2012-12-04 13:42:09 -05:00
Ross Lazarus 6a892b3555 Fix parameters for fastqc to work properly with bam and with a contaminants file 
Been b0rken for a long time - probably not much used..
 2012-10-26 16:00:13 +11:00
Jeremy Goecks 9fabf5dfbe Add feature/attribute name indexing framework to converters. Provide full text indexing for GFF attributes. 2012-08-16 16:32:00 -04:00
Scott McManus e069425ab9 Removed offending code from last checkin - sorry for the foul-up 2012-08-07 13:35:39 -04:00
Scott McManus 92915592f9 Added minor changes, including model accessors, for cancelling PBS tasks 2012-08-05 23:45:11 -04:00
Jeremy Goecks df28aec040 Full and proper sorting for GTF datasets: sort by, in order, transcript_id, chrom, and start. 2012-05-24 13:26:48 -04:00
Daniel Blankenberg 7c930f1c92 Tool help updates. 2011-11-14 13:26:29 -05:00
Daniel Blankenberg 9f9e55f320 Update sff extractor to version 0.2.10. 2011-10-20 16:38:14 -04:00
Daniel Blankenberg 940bb8d738 Some random lines tool tweaks. 2011-09-25 13:27:14 -04:00
Daniel Blankenberg 09e8a94a5a Rewrite random lines tool. Does two passes through input file: first pass determines line offsets/count, offsets are randomly removed, second pass writes out lines by seeking to remaining offsets. The random seed can now be optionally specified. 2011-09-23 13:49:33 -04:00
Daniel Blankenberg 727ce45cbf Fix tabs in secure_hash_message_digest.xml. 2011-09-09 12:15:27 -04:00
Daniel Blankenberg 9017c6fbd8 Add tool for calculating Secure Hashes / Message Digests of a dataset using the user selected algorithms. 2011-09-09 12:01:43 -04:00
Anton Nekrutenko d2d6956108 Patch from Peter Cock (bug534) for cut tool to ignore commented lines. 2011-06-08 17:17:11 -04:00
Jeremy Goecks 1d03c82144 Enable GFF filter attributes tool to accept arbitrary conditions. 2011-05-05 16:51:56 -04:00
Jeremy Goecks 7f034c56ac Fix bug in 'Filter GTF data by attribute values list' tool. 2011-05-03 09:45:40 -04:00
Jeremy Goecks 1a371da9ae Add tool 'Filter GTF by attribute values list.' Tool filters a GTF based on a list of attribute values; this tool is especially useful as a downstream analysis tool for filtering GTF files based on Cuffdiff outputs. Functional tests are included as well. 2011-04-11 09:39:55 -04:00
Richard Burhans f67ab3c70c fixed calculation of codon starts 2011-03-24 15:03:12 -04:00
Kanwei Li bfa19d9f64 Typos in tool confs 2011-03-21 13:48:28 -04:00
Jeremy Goecks 82ef98f15c Fix bugs in GFFReaderWrapper so that GFF3 files are read properly. Add GFF3 test to gff_filter_by_feature_count. 2011-03-09 14:22:10 -05:00
Jeremy Goecks 86b7194bff Use GFFReaderWrapper in gff_filter_by_feature_count tool in order to leverage support for GTF, GFF, and GFF3 found in reader wrapper. This also simplifies the tool considerably. 2011-03-08 19:01:59 -05:00
Jeremy Goecks 0030c2c810 Fix bug in output for gff_filter_by_feature_count tool. 2011-03-07 15:53:31 -05:00
Kanwei Li 096e95ff41 Typos 2011-02-25 13:35:27 -05:00
Kanwei Li 036082793b Fix bed_to_bigBed test 2011-02-24 15:23:21 -05:00
Jeremy Goecks ef28a2cb36 Set output dataset type for 'Extract GFF features' tool to be input dataset type. 2011-02-22 18:41:15 -05:00
Daniel Blankenberg 882b98531c Add a Line/Word/Character count Text Manipulation tool. 2011-02-15 17:24:24 -05:00