view degust.xml @ 2:1e4307fd98f3 draft

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<tool id="degust" name="Degust" version="1.0.0">
    <description>RNA Seq analysis and visualisation.</description>
    <command interpreter="python">
        degust.py
        --tab
        $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"/>
    </outputs>
    
    <help>
**Degust**
RNA Seq analysis and visualisation.

Written by David Powell - Victorian Bioinformatics Consortium 2012 - 2014

Wrapped by Simon Gladman - Victorian Bioinformatics Consortium 2014

0.11.2
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Outputs in html format.
    
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Inputs:

Gene differential expression dataset

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# 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>