diff readme.rst @ 16:d9a0a017896a draft

Uploaded

--- a/readme.rst	Fri Jan 24 11:18:29 2014 -0500
+++ b/readme.rst	Sat Feb 15 15:41:04 2014 -0500
@@ -1,60 +1,61 @@
 ========================
-Galaxy wrapper for MACS2
+Galaxy deeptools wrapper
 ========================
 
-With the improvement of sequencing techniques, chromatin immunoprecipitation 
-followed by high throughput sequencing (ChIP-Seq) is getting popular to study 
-genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq 
-analysis method, we present a novel algorithm, named Model-based Analysis of 
-ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures 
-the influence of genome complexity to evaluate the significance of enriched ChIP 
-regions, and MACS improves the spatial resolution of binding sites through 
-combining the information of both sequencing tag position and orientation. 
-MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
+deepTools are user-friendly tools for the normalization and visualization of 
+deep-sequencing data.
+They address the challenge of visualizing the large amounts of data that are now
+routinely generated from sequencing centers in a meaningful way. 
+To do so, deepTools contain useful routines to process the mapped reads data 
+through removal of duplicates and different filtering options to create coverage
+files in standard bedGraph and bigWig file formats. deepTools allow the creation
+of normalized coverage files or the comparison between two files 
+(for example, treatment and control). Finally, using such normalized and 
+standardized files, multiple visualizations can be created to identify 
+enrichments with functional annotations of the genome. 
+For a gallery of images that can be produced and a description 
+of the tools see our poster_.
+
+.. _poster: http://f1000.com/posters/browse/summary/1094053
+
+deeptools is developed under here:
+
+    https://github.com/fidelram/deepTools
+
+For support, questions, or feature requests contact: [e-mail]
 
 
-============
-Installation
-============
+========
+Citation
+========
 
-It is recommended to install this wrapper via the `Galaxy Tool Shed`.
-
-.. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
+deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
 
 
 =======
 History
 =======
-- v2.0.10.1: Initial public release
-- v2.0.10.3: add "broad peaks" options
 
-
-====================
-Detailed description
-====================
-
-View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README.rst
+- v1.0: Initial public release
 
 
-===============================
-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
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-
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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