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1 <tool id="prop_venn" name="proportional venn" version="0.4">
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2 <description> from 2-3 sets</description>
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3 <command interpreter="python">venner.py
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4 #if str( $twoThree['tt']) == 'three':
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5 --files $inputFile1,$inputFile2,$twoThree.inputFile3
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6 --columns $column1,$column2,$twoThree.column3
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7 --asNames $asName1,$asName2,$twoThree.asName3
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8 #else:
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9 --file $inputFile1,$inputFile2
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10 --columns $column1,$column2
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11 --asNames $asName1,$asName2
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12 #end if
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13 --title '$title'
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14 --size $size
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15 --outname $outPath
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16 </command>
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17 <inputs>
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18 <param name="title" label="title" type="text" help="title of plot" optional="true" value=""/>
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19 <param name="name" label="name" type="text" help="name of output file" value="venn of NA"/>
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20 <param name="size" label="size" type="integer" help="size of plot ( < 540)" optional="true" value="300"/>
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21
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22 <param format="tabular" name="inputFile1" label="input file 1" type="data" help="tabular input file" optional="false"/>
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23 <param name="column1" label="column index" type="integer" help="0 based index of element column" optional="false" value="0"/>
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24 <param name="asName1" label="as name" type="text" help="nice name for columns on plot" optional="false" value="A"/>
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25
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26 <param format="tabular2" name="inputFile2" label="input file 2" type="data" help="tabular input file" optional="false"/>
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27 <param name="column2" label="column index file 2" type="integer" help="0 based index of element column" optional="false" value="0"/>
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28 <param name="asName2" label="as name file 2" type="text" help="nice name for columns on plot" optional="false" value="B"/>
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29
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30 <conditional name="twoThree">
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31 <param name="tt" type="select" label="two or three">
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32 <option value="two" selected="true">two</option>
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33 <option value="three">three</option>
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34 </param>
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35 <when value="two">
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36 </when>
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37 <when value="three">
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38 <param format="tabular" name="inputFile3" label="input file 3" type="data" help="tabular input file" optional="false"/>
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39 <param name="column3" label="column index file 3" type="integer" help="0 based index of element column" optional="false" value="0"/>
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40 <param name="asName3" label="as name file 3" type="text" help="nice name for columns on plot" optional="false" value="C"/>
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41 </when>
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42 </conditional>
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43 </inputs>
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44
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45 <outputs>
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46 <data name="outPath" format="html" label="${name}"/>
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47 </outputs>
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48
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49 <help>
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50
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51 Proportional Venn Diagram:
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52 --------------------------
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53 Creates a proportional Venn diagram from 2 or 3 tab delimited input files.
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54 The 0 based column index decides which column is used for extracting the sets to compare between the files.
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55 Multiple items with the same value per column are counted as one.
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56
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57 Requirements:
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58 -------------
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59 - 2-3 tab delimited input files.
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60 - 0 based index of the columns to extract for each file
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61
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62 Outputs:
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63 --------
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64 - Html page with the proportional Venn diagram and a table for the counts in each section.
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65
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66 Please turn to *Ido Tamir* in case of problems or suggestions for this tool.
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67
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68
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69
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70 </help>
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71
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72 </tool>
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73
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74
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