diff rgclustal/README @ 0:8888e4e3f169

Migrated tool version 0.1 from old tool shed archive to new tool shed repository

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+This is a wrapper for ClustalW.
+
+This tool allows you to align multiple sequences in Galaxy, using ClustalW2_ with mostly default options which should work reasonably well for many alignments.
+DNA or protein sequences can be aligned. The input file must be a fasta file in your current history.
+
+The alignments will appear as a clustal format file or optionally, as phylip or fasta format files in your history and a text log will be output to your history 
+showing the output Clustalw would normally write to standard output.
+
+If Clustal format is chosen, you have the option of adding basepair counts to the output
+
+A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output 
+
+**Installation**
+
+Make sure clustalw2 is available on the path for all your nodes
+
+Move the test data files to your galaxy root test-data
+Move the xml file to a subdirectory of your tools folder (eg rgenetics/) and then add a line in your tool_conf.xml to point there.
+Run
+sh run_functional_tests.sh -id clustalw
+to make sure the tests work
+
+then restart Galaxy and you should be good to go.
+
+**Attribution**
+
+Clustal attribution and associated documentation are available at http://www.clustal.org
+
+An implementation of a Galaxy Clustal wrapper was written by Hans-Rudolf Hotz in an email on the developer list - 
+http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
+
+This version by Ross Lazarus for the rgenetics project, builds on Hans-Rudolf's code, adding some additional controls and a log file. It also
+deals with stderr so Cluastalw2 writing there doesn't cause the job to error out. That's encoded in the tail of the command line. 
+
+**License**
+
+Assuming Hans-Rudolf is ok with a new license for this derived work, this version of his wrapper is LGPL like other rgenetics artefacts
+
+Written by Ross Lazarus for the Rgenetics project
+
+Copyright Ross Lazarus at gmail com 2011
+
+All rights reserved.
+
+Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html
+
+
+
+