README.md in genomer-plugin-summary-0.0.4 vs README.md in genomer-plugin-summary-0.0.5
- old
+ new
@@ -1,29 +1,67 @@
-# Genomer::Plugin::Summary
+
-TODO: Write a gem description
+## About
+Summary is a plugin for the [genomer][] tool for genome finishing. This summary
+plugin provides metrics that useful are to understanding that state of your
+genome scaffold. Plugins are added to a genomer project by specifying them in
+the project Gemfile. Each summary function is documented with a [manual
+page][man].
+
+[genomer]: https://github.com/michaelbarton/genomer
+[man]: https://github.com/michaelbarton/genomer-plugin-summary/tree/master/man
+
+## Usage
+
+The following command will provide a list of all the gaps in your genome
+scaffold:
+
+ $ genomer summary gaps
+
+Producing output similiar to as follows:
+
+ +----------+----------+----------+----------+--------------+
+ | Scaffold Gaps |
+ +----------+----------+----------+----------+--------------+
+ | Number | Length | Start | End | Type |
+ +----------+----------+----------+----------+--------------+
+ | 1 | 400 | 121250 | 121649 | unresolved |
+ | 2 | 659 | 123354 | 124012 | contig |
+ | 3 | 10 | 126781 | 126790 | unresolved |
+ | 4 | 10 | 127393 | 127402 | unresolved |
+ | 5 | 500 | 778936 | 779435 | unresolved |
+ | 6 | 659 | 781140 | 781798 | contig |
+ | 7 | 10 | 784567 | 784576 | unresolved |
+ | 8 | 300 | 785179 | 785478 | unresolved |
+ | 9 | 556 | 803968 | 804523 | contig |
+ | 10 | 242 | 1032294 | 1032535 | contig |
+ | 11 | 1751 | 1057108 | 1058858 | contig |
+ | 12 | 575 | 1137194 | 1137768 | contig |
+ <remainder omitted>
+
+Other commands are available for showing contigs, sequences, and the complete
+scaffolded genome. These are listed in the [manual page][man] directory.
+
## Installation
-Add this line to your application's Gemfile:
+Add this line to your genomer projects's Gemfile:
gem 'genomer-plugin-summary'
-And then execute:
+And then execute in the project directory:
$ bundle
-Or install it yourself as:
+Run the `help` command and the summary plugin should be available:
- $ gem install genomer-plugin-summary
+ $ genomer help
+ $ genomer man summary
-## Usage
+## Copyright
-TODO: Write usage instructions here
+Genomer copyright (c) 2010 by Michael Barton. Genomer is licensed under the MIT
+license. See LICENSE.txt for further details. The tape measure image is used
+under a Creative Commons Generic 2.0 Licence. The original can be [found on
+flickr.][flickr]
-## Contributing
-
-1. Fork it
-2. Create your feature branch (`git checkout -b my-new-feature`)
-3. Commit your changes (`git commit -am 'Added some feature'`)
-4. Push to the branch (`git push origin my-new-feature`)
-5. Create new Pull Request
+[flickr]: http://www.flickr.com/photos/aussiegall/286709039/