diff readme.rst @ 25:d2898b81b912 draft

Uploaded

--- a/readme.rst	Tue Feb 04 09:12:07 2014 -0500
+++ b/readme.rst	Tue Feb 04 13:45:17 2014 -0500
@@ -1,61 +1,41 @@
-========================
-Galaxy deeptools wrapper
-========================
+This package contains a collection of Galaxy workflows utilising deepTools.
 
-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]
+See http://www.galaxyproject.org for information about the Galaxy Project.
 
 
-========
+Sample Data
+===========
+
+Sample data can be obtained from http://deeptools.ie-freiburg.mpg.de/library or you
+can use aligned reads in BAM or SAM format.
+
+
+
 Citation
 ========
 
-deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
-
+If you use this workflow directly, or a derivative of it, or the associated
+deepTools wrappers for Galaxy, in work leading to a scientific publication,
+please cite:
 
-=======
-History
-=======
-
-- v1.0: Initial public release
+{publication under review}
 
 
-Licence (MIT)
-=============
+Availability
+============
 
-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:
+This workflow is available on the main Galaxy Tool Shed:
+
+http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows
+
+Development is being done on github:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+https://github.com/fidelram/deepTools
+
 
-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.
+Dependencies
+============
+
+These dependencies should be resolved automatically via the Galaxy Tool Shed:
+
+* http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools