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+
+X!TANDEM LICENSE AND README ===========================================
+
+
+ X! tandem protein sequence modeler
+
+  What is it?
+  -----------
+  X! tandem open source software that can model tandem
+  mass spectra with protein sequences. This software
+  has a very simple, unsophistocated application programming
+  interface (API): it simply takes an XML file of instructions
+  on its command line, and output the results into an XML file,
+  which has been specified in the input XML file. 
+  
+  The Latest Version
+  ------------------
+
+  Details of the latest version can be found on the X! tandem
+  project page under http://www.thegpm.org. 
+  This version is the first release the CYCLONE edition (version 2012.10.01.1).
+
+
+  Documentation
+  -------------
+
+  This version of X! tandem is a full release, only including source
+  level documentation. As more releases occur, better documentation
+  will be included.
+
+  Installation
+  ------------
+
+  (IN this case installation is automatically done by Galaxy's Toolshed).
+
+  Licensing
+  ---------
+
+	The Artistic License for all X! software, binaries and documentation
+
+	Preamble
+	The intent of this document is to state the conditions under which a
+	Package may be copied, such that the Copyright Holder maintains some 
+	semblance of artistic control over the development of the package, 
+	while giving the users of the package the right to use and distribute 
+	the Package in a more-or-less customary fashion, plus the right to 
+	make reasonable modifications. 
+
+	Definitions
+	"Package" refers to the collection of files distributed by the Copyright 
+	  Holder, and derivatives of that collection of files created through 
+	  textual modification. 
+
+	"Standard Version" refers to such a Package if it has not been modified, 
+	  or has been modified in accordance with the wishes of the Copyright 
+	  Holder as specified below. 
+
+	"Copyright Holder" is whoever is named in the copyright or copyrights 
+	  for the package. 
+
+	"You" is you, if you're thinking about copying or distributing this Package. 
+
+	"Reasonable copying fee" is whatever you can justify on the basis of 
+	  media cost, duplication charges, time of people involved, and so on. 
+	  (You will not be required to justify it to the Copyright Holder, but 
+	  only to the computing community at large as a market that must bear 
+	  the fee.) 
+
+	"Freely Available" means that no fee is charged for the item itself, 
+	  though there may be fees involved in handling the item. It also means 
+	  that recipients of the item may redistribute it under the same
+	  conditions they received it. 
+
+	1. You may make and give away verbatim copies of the source form of the 
+	Standard Version of this Package without restriction, provided that 
+	you duplicate all of the original copyright notices and associated 
+	disclaimers. 
+
+	2. You may apply bug fixes, portability fixes and other modifications 
+	derived from the Public Domain or from the Copyright Holder. A 
+	Package modified in such a way shall still be considered the Standard 
+	Version. 
+
+	3. You may otherwise modify your copy of this Package in any way, provided 
+	that you insert a prominent notice in each changed file stating how and 
+	when you changed that file, and provided that you do at least ONE of the 
+	following: 
+
+	  a. place your modifications in the Public Domain or otherwise make them 
+		 Freely Available, such as by posting said modifications to Usenet 
+		 or an equivalent medium, or placing the modifications on a major 
+		 archive site such as uunet.uu.net, or by allowing the Copyright Holder 
+		 to include your modifications in the Standard Version of the Package. 
+	  b. use the modified Package only within your corporation or organization. 
+	  c. rename any non-standard executables so the names do not conflict 
+		 with standard executables, which must also be provided, and provide 
+		 a separate manual page for each non-standard executable that clearly 
+		 documents how it differs from the Standard Version. 
+	  d. make other distribution arrangements with the Copyright Holder. 
+
+	4. You may distribute the programs of this Package in object code or 
+	executable form, provided that you do at least ONE of the following: 
+
+	  a. distribute a Standard Version of the executables and library files, 
+		 together with instructions (in the manual page or equivalent) on 
+		 where to get the Standard Version. 
+	  b. accompany the distribution with the machine-readable source of the 
+		 Package with your modifications. 
+	  c. give non-standard executables non-standard names, and clearly 
+		 document the differences in manual pages (or equivalent), together 
+		 with instructions on where to get the Standard Version. 
+	  d. make other distribution arrangements with the Copyright Holder. 
+
+	5. You may charge a reasonable copying fee for any distribution of 
+	this Package. You may charge any fee you choose for support of 
+	this Package. You may not charge a fee for this Package itself. 
+	However, you may distribute this Package in aggregate with other 
+	(possibly commercial) programs as part of a larger (possibly 
+	commercial) software distribution provided that you do not a
+	dvertise this Package as a product of your own. You may embed this 
+	Package's interpreter within an executable of yours (by linking); 
+	this shall be construed as a mere form of aggregation, provided that 
+	the complete Standard Version of the interpreter is so embedded. 
+
+	6. The scripts and library files supplied as input to or produced as 
+	output from the programs of this Package do not automatically fall 
+	under the copyright of this Package, but belong to whomever generated 
+	them, and may be sold commercially, and may be aggregated with this 
+	Package. If such scripts or library files are aggregated with this 
+	Package via the so-called "undump" or "unexec" methods of producing 
+	a binary executable image, then distribution of such an image shall 
+	neither be construed as a distribution of this Package nor shall it 
+	fall under the restrictions of Paragraphs 3 and 4, provided that you 
+	do not represent such an executable image as a Standard Version of 
+	this Package. 
+
+	7. C subroutines (or comparably compiled subroutines in other languages) 
+	supplied by you and linked into this Package in order to emulate 
+	subroutines and variables of the language defined by this Package 
+	shall not be considered part of this Package, but are the equivalent 
+	of input as in Paragraph 6, provided these subroutines do not change 
+	the language in any way that would cause it to fail the regression 
+	tests for the language. 
+
+	8. Aggregation of this Package with a commercial distribution is always 
+	permitted provided that the use of this Package is embedded; that is, 
+	when no overt attempt is made to make this Package's interfaces visible 
+	to the end user of the commercial distribution. Such use shall not be 
+	construed as a distribution of this Package. 
+
+	9. The name of the Copyright Holder may not be used to endorse or promote 
+	products derived from this software without specific prior written permission. 
+
+	10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED 
+	WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF 
+	MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. 
+
+	The End 
+
+
+  Contacts
+  --------
+
+  For any questions involving X! tandem, please contact 
+  contact@thegpm.org
+
+  Acknowledgments
+  ----------------
+
+  Ron Beavis - system design and implementation
+  Rob Craig - debugging and LINUX implementation
+  Jayson Falkner - code for GeeToo LINUX implementation
+  Patrick Lacasse - initial additions for mzxml and mzdata functionality
+  Brendan McLean - optimized changes for mzxml and mzdata functionality using expat library
+
+
+