diff readme.rst @ 17:35a80f8dda5c draft

Uploaded

--- a/readme.rst	Sat Feb 15 15:41:04 2014 -0500
+++ b/readme.rst	Sat Feb 15 15:43:39 2014 -0500
@@ -1,61 +1,60 @@
 ========================
-Galaxy deeptools wrapper
+Galaxy wrapper for MACS2
 ========================
 
-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]
+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.
 
 
-========
-Citation
-========
+============
+Installation
+============
 
-deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
+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
 
 
 =======
 History
 =======
+- v2.0.10.1: Initial public release
+- v2.0.10.3: add "broad peaks" options
 
-- v1.0: Initial public release
+
+====================
+Detailed description
+====================
+
+View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README.rst
 
 
-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:
+===============================
+Wrapper Licence (MIT/BSD style)
+===============================
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+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 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.
+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.
+