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comparison degust.xml @ 2:1e4307fd98f3 draft

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author simon-gladman
date Mon, 24 Feb 2014 19:02:18 -0500
parents 504bf58a4022
children a50be29ea995
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1:773107d91822 2:1e4307fd98f3
1 <tool id="degust" name="Degust" version="1.0.0"> 1 <tool id="degust" name="Degust" version="1.0.0">
2 <description>RNA Seq analysis and visualisation.</description> 2 <description>RNA Seq analysis and visualisation.</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 degust.py 4 degust.py
5 --tab 5 --tab
6 --cuffdiff 6 $cuffdiff
7 $dataset 7 $dataset
8 > 8 >
9 $output 9 $output
10 </command> 10 </command>
11 <inputs> 11 <inputs>
12 <param name="dataset" type="data" format="tabular" label="Cuffdiff gene/transcript expression testing output" help="Cuffdiff output to visualise."/> 12 <param name="dataset" type="data" format="tabular" label="Cuffdiff gene/transcript expression testing output" help="Cuffdiff output to visualise."/>
13 <param name="cuffdiff" type="boolean" truevalue="--cuffdiff" falsevalue="" checked="true" label="Cuffdiff output" help="Is this cuffdiff output?"/>
13 </inputs> 14 </inputs>
14 <outputs> 15 <outputs>
15 <data name="output" format="html" label="${tool.name} on ${on_string}: html"/> 16 <data name="output" format="html" label="${tool.name} on ${on_string}: html"/>
16 </outputs> 17 </outputs>
17 18
30 31
31 ------ 32 ------
32 33
33 Inputs: 34 Inputs:
34 35
35 CuffDiff gene differential expression dataset 36 Gene differential expression dataset
37
38 ------
39
40 # Degust (formerly known as DGE-Vis)
41
42 * Visualise RNA-seq differential expression data.
43 * Perform your own DGE analysis to analyse from your own "counts" file.
44
45 Access a public web service running [Degust](http://www.vicbioinformatics.com/degust).
46
47 View a [short video](https://www.youtube.com/watch?v=ucucQ_LtZ1g) of the interface in use.
48
49 Read a summary on the <a href='http://victorian-bioinformatics-consortium.github.io/degust/'>Degust home page</a>.
50
51
52 ## Contributing ##
53 Feel free to contribute with pull requests, bug reports or enhancement suggestions.
54
55 ## Known Issues
56
57 #### Heatmap
58
59 * Clustering algorithm is naive greedy N^2. So, not fast, and not a great clustering.
60
61 ## License ##
62 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>
36 </help> 63 </help>
37 </tool> 64 </tool>