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1 <tool id="Vennerable" name="Vennerable" version="0.9" >
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2 <description>: Plot data in Venn or Venn-like diagrams</description>
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3 <command>
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4 #if $opt.userSpecified == "Yes"
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5 R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R
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6 --args $inputFile
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7 default
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8 $weighting
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9 $outputFile
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10 $plottype
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11 $resolution
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12 2>$Vennerable_log
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13 1>>$Vennerable_log
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14 #else
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15 R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R
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16 --args $inputFile
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17 "$opt.xNames"
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18 $weighting
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19 $outputFile
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20 $plottype
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21 $resolution
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22 2>$Vennerable_log
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23 1>>$Vennerable_log
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24 #end if
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25 </command>
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26 <inputs>
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27 <param name="inputFile" format="tabular" type="data" label="Data set" />
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28 <conditional name="opt">
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29 <param name="userSpecified" type="select" label="Use column headers as dataset names?">
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30 <option value="Yes">Yes</option>
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31 <option value="No">No</option>
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32 </param>
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33 <when value="Yes">
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34 </when>
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35 <when value="No">
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36 <param name="xNames" type="text" label="Alternative data names" value="A,B,C,D" help="(comma-separated)"/>
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37 </when>
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38 </conditional>
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39 <param name="plottype" type="select" label="Plot type to use" help="some other options might get disabled for certain plottypes" >
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40 <option value="AWFE" selected="True">AWFE: Edwards-Venn (Non-weighted)</option>
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41 <option value="ChowRuskey">Chow-Ruskey (always weigthed)</option>
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42 <option value="ellipses">Ellipses (4 datasets only and always non-weighted)</option>
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43 <option value="circles">Circles (max 3 datasets)</option>
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44 <option value="squares">Squares (max 4 datasets non-weighted)</option>
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45 </param>
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46 <param name="weighting" type="select" label="Use weighting for data in plot" >
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47 <option value="FALSE" selected="True">Non-weighted</option>
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48 <option value="TRUE">Weighted</option>
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49 </param>
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50 <param name="resolution" type="integer" label="Resolution to use (dpi)" value="150" help="Plot features can be sized with this setting. Lower (50) is larger text." />
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51 </inputs>
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52 <outputs>
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53 <data name="outputFile" format="png" label="Venn diagram of ${inputFile.name}"/>
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54 <data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" />
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55 </outputs>
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56 <tests>
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57 <test>
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58 </test>
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59 </tests>
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60 <requirements>
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61 <requirement type="binary">R</requirement>
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62 </requirements>
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63 <help>
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64 |
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65
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66
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67 **What it does**
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68
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69 Vennerable V2.0 (09-10-2009)
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70
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71 This tool will use the Vennerable R package to plot data as weighted or un-weighted diagrams such as Venn, Edwards-Venn and Chow-Rusky.
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72
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73 The tool can take 2 to 7 collumns of data but more are adviced not to be used (for speed and clarity).
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74
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75 -----
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76
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77 **Input**
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78
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79 It takes a tabular file containing identifiers. Matches will be calculated automatically.
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80
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81 Be sure to specify headers if you haven't any in your dataset! Otherwise the top row of data will be excluded.
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82
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83 ::
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84
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85 DataA DataB DataC DataD
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86 HUM1 AGK2 AGK2 RTT3
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87 AGK2 ZZE3 ERT3 ZPD3
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88 ZPD3 AAW3 RTT3 WER2
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89 WER2 HUM1 RRW4 DUM1
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90
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91 -----
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92
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93 **Example**
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94
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95 .. image:: ../static/images/WURtools/VennerablePlot.png
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96
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97 -----
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98
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99 **References**
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100
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101 - alex.bossers@wur.nl
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102 - Vennerable R package: http://r-forge.r-project.org/projects/vennerable/
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103
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104 -----
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105
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106 .. class:: infomark
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107
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108 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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109
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110
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111 </help>
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112 </tool>
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