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1 <tool id="Vennerable" name="Vennerable" version="1.2c" >
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2 <description>: Plot data in Venn or Edwards/Venn-like diagrams</description>
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3 <command>
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4 R --slave --vanilla --file=\$VENNERABLE_SCRIPT_PATH/vennerable/Vennerable.R
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5 --args $inputFile
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6 #if $opt.userSpecified == "Yes"
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7 default
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8 #else
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9 "$opt.xNames"
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10 #end if
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11 $weighting
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12 #if $imagetype.value == "svg"
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13 $outputFile_svg
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14 $plottype
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15 $resolution
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16 svg
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17 #else if $imagetype.value == "png"
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18 $outputFile_png
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19 $plottype
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20 $resolution
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21 png
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22 #else
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23 $outputFile_pdf
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24 $plottype
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25 $resolution
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26 pdf
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27 #end if
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28 2>$Vennerable_log
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29 1>>$Vennerable_log
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30 </command>
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31 <inputs>
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32 <param name="inputFile" format="tabular" type="data" label="Data set" />
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33 <conditional name="opt">
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34 <param name="userSpecified" type="select" label="Use column headers as dataset names?">
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35 <option value="Yes">Yes</option>
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36 <option value="No">No</option>
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37 </param>
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38 <when value="Yes">
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39 </when>
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40 <when value="No">
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41 <param name="xNames" type="text" label="Alternative data names" value="A,B,C,D" help="(comma-separated)"/>
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42 </when>
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43 </conditional>
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44 <param name="plottype" type="select" label="Plot type to use" help="some other options might get disabled for certain plottypes" >
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45 <option value="AWFE" selected="True">AWFE: Edwards-Venn (Non-weighted up to 5 datasets)</option>
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46 <option value="ChowRuskey">Chow-Ruskey (always weigthed max 9 sets common intersect not 0)</option>
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47 <option value="ellipses">Ellipses (4 datasets only and always non-weighted)</option>
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48 <option value="circles">Circles (max 3 datasets)</option>
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49 <option value="squares">Squares (max 4 datasets non-weighted)</option>
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50 <option value="battle">Edwards-Venn Squares battle (max 9 datasets, non-weighted)</option>
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51 </param>
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52 <param name="weighting" type="select" label="Use weighting for data in plot" >
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53 <option value="FALSE" selected="True">Non-weighted</option>
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54 <option value="TRUE">Weighted</option>
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55 </param>
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56 <param name="resolution" type="integer" label="Resolution to use (dpi)" value="150" help="Plot features can be sized with this setting (PNG only). Lower (50) is larger text.<br /><i>Default is vector graphics format SVG!</i>" />
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57 <param name="imagetype" type="select" label="Image output format" help="Scalable Vector Graphics (SVG) format is best for post processing" >
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58 <option value="pdf" selected="True">PDF</option>
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59 <option value="svg">SVG</option>
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60 <option value="png">PNG</option>
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61 </param>
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62 </inputs>
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63 <outputs>
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64 <data name="outputFile_svg" format="svg" label="Venn diagram svg of ${inputFile.name}">
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65 <filter>imagetype=="svg"</filter>
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66 </data>
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67 <data name="outputFile_png" format="png" label="Venn diagram png of ${inputFile.name}">
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68 <filter>imagetype=="png"</filter>
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69 </data>
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70 <data name="outputFile_pdf" format="pdf" label="Venn diagram pdf of ${inputFile.name}">
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71 <filter>imagetype=="pdf"</filter>
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72 </data>
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73 <data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" />
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74 </outputs>
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75 <tests>
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76 <test>
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77 </test>
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78 </tests>
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79 <requirements>
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80 <requirement type="package" version="3.0.3">R</requirement>
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81 <requirement type="package" version="1.0">vennerable_r_packages</requirement>
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82 <requirement type="set_environment">VENNERABLE_SCRIPT_PATH</requirement>
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83 </requirements>
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84 <help>
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85 |
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86
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87
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88 **What it does**
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89
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90 Vennerable V3.0 (07-10-2014)
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91
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92 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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93
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94 The tool can take from 2 to 9 collumns (in battle mode) of data but more are adviced not to be used (for speed and clarity).
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95
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96 Since version Vennerable version 3 it supports up to 9 datasets in battle mode. Wrapper version 1.2 and up support output in svg, pdf and png.
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97
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98 -----
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99
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100 **Input**
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101
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102 It takes a tabular file containing identifiers. Matches will be calculated automatically.
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103
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104 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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105
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106 ::
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107
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108 DataA DataB DataC DataD
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109 HUM1 AGK2 AGK2 RTT3
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110 AGK2 ZZE3 ERT3 ZPD3
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111 ZPD3 AAW3 RTT3 WER2
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112 WER2 HUM1 RRW4 DUM1
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113
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114 -----
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115
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116 **Example**
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117
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118 .. image:: ../static/images/WURtools/VennerablePlot.png
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119
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120 -----
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121
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122 **References**
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123
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124 - alex.bossers@wur.nl
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125 - Vennerable R package: http://r-forge.r-project.org/projects/vennerable/
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126
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127 -----
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128
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129 .. class:: infomark
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130
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131 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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132
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133
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134 </help>
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135 </tool>
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