# HG changeset patch
# User simon-gladman
# Date 1393286538 18000
# Node ID 1e4307fd98f3a53c6194caf33995a8638f21693d
# Parent  773107d9182215ac330fbd2fac1d53fec906e5a6
Uploaded

diff -r 773107d91822 -r 1e4307fd98f3 degust.xml
--- a/degust.xml	Mon Feb 24 00:41:33 2014 -0500
+++ b/degust.xml	Mon Feb 24 19:02:18 2014 -0500
@@ -3,13 +3,14 @@
     <command interpreter="python">
         degust.py
         --tab
-        --cuffdiff
+        $cuffdiff
         $dataset
         > 
         $output
     </command>
     <inputs>
         <param name="dataset" type="data" format="tabular" label="Cuffdiff gene/transcript expression testing output" help="Cuffdiff output to visualise."/>
+        <param name="cuffdiff" type="boolean" truevalue="--cuffdiff" falsevalue="" checked="true" label="Cuffdiff output" help="Is this cuffdiff output?"/>
     </inputs>
     <outputs>
         <data name="output" format="html" label="${tool.name} on ${on_string}: html"/>
@@ -32,6 +33,32 @@
 
 Inputs:
 
-CuffDiff gene differential expression dataset
+Gene differential expression dataset
+
+------
+
+# Degust (formerly known as DGE-Vis)
+
+* Visualise RNA-seq differential expression data.
+* Perform your own DGE analysis to analyse from your own "counts" file.
+
+Access a public web service running [Degust](http://www.vicbioinformatics.com/degust).
+
+View a [short video](https://www.youtube.com/watch?v=ucucQ_LtZ1g) of the interface in use.
+
+Read a summary on the <a href='http://victorian-bioinformatics-consortium.github.io/degust/'>Degust home page</a>.
+
+
+## Contributing ##
+Feel free to contribute with pull requests, bug reports or enhancement suggestions.
+
+## Known Issues
+
+#### Heatmap 
+
+  * Clustering algorithm is naive greedy N^2.  So, not fast, and not a great clustering. 
+
+## License ##
+Degust is released under the GPL v3 (or later) license, see <a href='http://github.com/Victorian-Bioinformatics-Consortium/degust/blob/master/COPYING.txt'>COPYING.txt</a>
     </help>
 </tool>