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1 <tool id="degust" name="Degust" version="1.0.0">
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2 <description>RNA Seq analysis and visualisation.</description>
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3 <command interpreter="python">
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4 degust.py
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5 --tab
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6 $cuffdiff
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7 $dataset
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8 >
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9 $output
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10 </command>
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11 <inputs>
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12 <param name="dataset" type="data" format="tabular" label="Cuffdiff gene/transcript expression testing output" help="Cuffdiff output to visualise."/>
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13 <param name="cuffdiff" type="boolean" truevalue="--cuffdiff" falsevalue="" checked="true" label="Cuffdiff output" help="Is this cuffdiff output?"/>
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14 </inputs>
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15 <outputs>
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16 <data name="output" format="html" label="${tool.name} on ${on_string}: html"/>
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17 </outputs>
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18
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19 <help>
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20 **Degust**
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21 RNA Seq analysis and visualisation.
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22
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23 Written by David Powell - Victorian Bioinformatics Consortium 2012 - 2014
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24
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25 Wrapped by Simon Gladman - Victorian Bioinformatics Consortium 2014
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26
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27 0.11.2
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28 ------
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29
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30 Outputs in html format.
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31
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32 ------
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33
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34 Inputs:
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35
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36 Gene differential expression dataset
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37
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38 ------
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39
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40 # Degust (formerly known as DGE-Vis)
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41
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42 * Visualise RNA-seq differential expression data.
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43 * Perform your own DGE analysis to analyse from your own "counts" file.
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44
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45 Access a public web service running [Degust](http://www.vicbioinformatics.com/degust).
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46
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47 View a [short video](https://www.youtube.com/watch?v=ucucQ_LtZ1g) of the interface in use.
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48
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49 Read a summary on the Degust home page (http://victorian-bioinformatics-consortium.github.io/degust/).
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50
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51
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52 ## Contributing ##
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53 Feel free to contribute with pull requests, bug reports or enhancement suggestions.
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54
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55 ## Known Issues
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56
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57 #### Heatmap
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58
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59 * Clustering algorithm is naive greedy N^2. So, not fast, and not a great clustering.
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60
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61 ## License ##
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62 Degust is released under the GPL v3 (or later) license, see http://github.com/Victorian-Bioinformatics-Consortium/degust/blob/master/COPYING.txt
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63 </help>
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64 </tool>
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