diff interproscan5/readme.rst @ 0:fe8e43a26870 draft

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date Thu, 28 Jan 2016 19:34:51 -0500
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+==================================================
+Galaxy wrapper for InterProScan 5 prediction tools
+==================================================
+
+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 2013 by:
+ * Bjoern Gruening
+ * Konrad Paszkiewicz
+
+
+This prepository contains a wrapper for the InterProScan_ command line tool.
+
+.. _InterProScan: http://www.ebi.ac.uk/interpro/interproscan.html
+
+
+Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. (2005). InterProScan: protein domains identifier. Nucleic Acids Res. 33 (Web Server issue): W116-W120
+
+
+============
+Installation
+============
+
+Please download install InterProScan according to:
+
+https://code.google.com/p/interproscan/wiki/HowToDownload
+
+
+========
+Citation
+========
+
+If you use this Galaxy tool in work leading to a scientific
+publication, in addition to citing the invididual underlying tools, please cite:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Full reference information is included in the help text.
+
+
+=============
+Input formats
+=============
+
+The standard interproscan input is either genomic or protein sequences. 
+In the case of genomic sequences Interproscan will run an ORF prediction tool.
+
+
+=======
+History
+=======
+
+interproscan:
+
+ - v5.0: Initial public release of version 5.0
+
+
+=============
+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:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the 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.
+