mothur_toolsuite: revision graph

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Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information. default tip
Mon, 10 Nov 2014 15:40:02 -0500, by galaxyuser
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
Fri, 31 Oct 2014 15:09:32 -0400, by certain cat
Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
Mon, 22 Sep 2014 11:19:09 -0400, by pjbriggs
mothur_wrapper.py - convert_value needs to return a String
Wed, 11 Sep 2013 16:56:31 -0500, by Jim Johnson
Fixes courtesy of Peter Briggs:
Wed, 04 Sep 2013 10:51:34 -0500, by Jim Johnson
Patches courtesy of Peter Briggs, Bioinformatics Core Facility University of Manchester
Tue, 30 Jul 2013 09:26:31 -0500, by Jim Johnson
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Thu, 30 May 2013 08:59:17 -0500, by Jim Johnson
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Tue, 28 May 2013 07:43:37 -0500, by Jim Johnson
mothur_wrapper.py - remove type restrictions for params - was failing for chimera.slayer
Wed, 20 Feb 2013 07:51:22 -0600, by Jim Johnson
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Tue, 04 Dec 2012 11:05:19 -0600, by Jim Johnson
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Wed, 16 May 2012 13:12:05 -0500, by Jim Johnson
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Wed, 16 May 2012 12:28:44 -0500, by Jim Johnson
Mothur - updates for Mothur version 1.24
Wed, 28 Mar 2012 15:45:03 -0500, by Jim Johnson
Mothur - eliminate warning message in mothur_count_groups
Thu, 19 Jan 2012 11:27:37 -0600, by Jim Johnson
Mothur - html escape amperand in calculator option label
Thu, 19 Jan 2012 10:34:04 -0600, by Jim Johnson
Changed np_shannon calcultor to npshannon and posted bug to mothur.org
Tue, 17 Jan 2012 14:42:27 -0600, by Jim Johnson
Remove obsolete suite_config.xml
Tue, 17 Jan 2012 14:18:35 -0600, by Jim Johnson
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Tue, 17 Jan 2012 14:16:44 -0600, by Jim Johnson
Mothur - update for Mothur version 1.23.0
Tue, 17 Jan 2012 11:22:44 -0600, by Jim Johnson
Modifications for ToolShed proprietary data types
Tue, 17 Jan 2012 11:08:15 -0600, by Jim Johnson
Mothur - fix set_meta for SffFlow in datatypes/metagenomics.py
Fri, 09 Dec 2011 12:12:16 -0600, by Jim Johnson
Mothur - updated for Mothur version 1.22.0
Tue, 08 Nov 2011 11:45:32 -0600, by Jim Johnson
Mothur - make.fastq fix command name and change_format on output fastq according to qual input, fastq.info outputs qual454
Wed, 05 Oct 2011 10:37:11 -0500, by Jim Johnson
Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
Wed, 05 Oct 2011 10:34:44 -0500, by Jim Johnson
Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
Tue, 09 Aug 2011 11:39:27 -0500, by Jim Johnson
Change make.shared param name from unique to groups
Thu, 14 Jul 2011 15:21:01 -0500, by Jim Johnson
Default value for skipgap params should be true
Fri, 08 Jul 2011 12:15:04 -0500, by Jim Johnson
Add name param to classify.otu
Fri, 08 Jul 2011 12:13:46 -0500, by Jim Johnson
trim.seqs name parameter needs to be optional
Tue, 05 Jul 2011 13:07:40 -0500, by Jim Johnson
Support Mothur v1.20
Mon, 27 Jun 2011 10:12:25 -0500, by Jim Johnson
Allow for output file ext to be either .chimera or .chimeras
Mon, 27 Jun 2011 09:34:14 -0500, by Jim Johnson
Add missing qual params to trim.seqs
Thu, 09 Jun 2011 16:24:30 -0500, by jj
set output formats to match input formats
Wed, 08 Jun 2011 15:02:44 -0500, by jjohnson
workflow cleanup_param_values recurses through paramnames whenever they start with a paramname_, so change input to input_fasta
Wed, 08 Jun 2011 14:59:08 -0500, by jj
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
Tue, 07 Jun 2011 17:39:06 -0400, by jjohnson
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
Tue, 07 Jun 2011 17:35:35 -0400, by jjohnson
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
Tue, 07 Jun 2011 17:32:23 -0400, by jjohnson

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