changeset 3:8ee90fc5fe11 draft

Uploaded

--- a/readme.rst	Wed Jul 10 14:53:51 2013 -0400
+++ b/readme.rst	Tue Oct 08 10:22:52 2013 -0400
@@ -1,17 +1,25 @@
-================================================
-Galaxy wrapper for InterProScan prediction tools
-================================================
+==================================================
+Galaxy wrapper for InterProScan 4 prediction tools
+==================================================
+
+**Note**:
+
+This wrapper is for InterProScan 4.x if you want to use InterProScan 5 please have a look at:
+http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5 
+
+-----
 
 InterProScan is a tool that combines different protein signature recognition methods native to the InterPro 
 member databases into one resource with look up of corresponding InterPro and GO annotation.
 
-This wrapper is copyright 2012-2013 by
-*  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
-*  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
+This wrapper is copyright 2012-2013 by:
+ *  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
+ *  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
 
 
-This prepository contains wrapper for the InterProScan command line tool.
-http://www.ebi.ac.uk/interpro/
+This prepository contains wrapper for the InterProScan_ command line tool.
+
+.. _InterProScan: http://www.ebi.ac.uk/interpro/
 
 
 Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8.
@@ -28,21 +36,25 @@
 Please see also:
 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html
 
-And rebuild the indizes if necessary:
+And rebuild the indizes if necessary
+
+.. code:: 
 
-index_data.pl -f interpro.xml -inx -v -bin -bforce
-index_data.pl -f match_complete.xml -inx -v -bin -bforce
-index_data.pl -f Pfam-A.seed -inx -v -bin -bforce
-index_data.pl -f Pfam-C -inx -v -bin -bforce
-index_data.pl -f prints.pval -inx -v -bin -bforce
-index_data.pl -f sf.seq -inx -v -bin -bforce
-index_data.pl -f sf_hmm -inx -v -bin -bforce
-index_data.pl -f smart.HMMs -inx -v -bin -bforce
-index_data.pl -f superfamily.hmm -inx -v -bin -bforce
-index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce
+	index_data.pl -f interpro.xml -inx -v -bin -bforce
+	index_data.pl -f match_complete.xml -inx -v -bin -bforce
+	index_data.pl -f Pfam-A.seed -inx -v -bin -bforce
+	index_data.pl -f Pfam-C -inx -v -bin -bforce
+	index_data.pl -f prints.pval -inx -v -bin -bforce
+	index_data.pl -f sf.seq -inx -v -bin -bforce
+	index_data.pl -f sf_hmm -inx -v -bin -bforce
+	index_data.pl -f smart.HMMs -inx -v -bin -bforce
+	index_data.pl -f superfamily.hmm -inx -v -bin -bforce
+	index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce
 
 
-Add the tool definition to your tool_conf.xml file under Galaxy root.
+Add the tool definition to your tool_conf.xml file under Galaxy root:
+.. code::
+
 	<tool file="iprscan/interproscan.xml" />
 
 =============
@@ -60,29 +72,30 @@
 =======
 
 interproscan:
-- v1.1: Initial public release
-- v1.2: Merge with Konrad Paszkiewicz repository
+
+ - v1.1: Initial public release
+ - v1.2: Merge with Konrad Paszkiewicz repository
 
 
-===============================
-Wrapper Licence (MIT/BSD style)
-===============================
+=============
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.