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1 <tool id="venn" name="Venn Diagram">
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2 <description>from summary counts</description>
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3 <command interpreter="python">$script_file $labels $counts $output $script</command>
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4 <inputs>
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5 <param name="labels" type="text" value="A,B" size="50" label="Set Labels"/>
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6 <param name="counts" type="text" value="30,10,20" size="80" label="Counts in each region" help="region order: two sets: A, B, AB; three sets: A,B,C,AB,BC,AC,ABC"/>
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7 </inputs>
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8 <configfiles>
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9 <configfile name="script_file">
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10 import os
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11 labels = '${labels}'.replace(' ','_').split(',')
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12 counts = '${counts}'.replace(' ','').split(',')
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13 counts = map(int,counts)
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14 rscript = open('${script}','w')
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15 rscript.write("options(warn=-1)\n")
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16 rscript.write("pdf('"+"${output}"+"')\n")
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17 rscript.write("library(grid)\n")
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18 rscript.write("library(VennDiagram)\n")
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19 if len(labels)==2:
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20 for i in range(2):
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21 counts[i+1] = counts[i+1]+counts[i]
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22 rscript.write("venn =venn.diagram(\n\tx=list(\n\t\t"+labels[0]+"=c(1:"+str(counts[0])+","+str(counts[1]+1)+":"+str(counts[2])+"),\n\t\t"+labels[1]+"="+str(counts[0]+1)+":"+str(counts[2])+"),\n\tfilename=NULL,\n\tfill=c('red','blue'),\n\tcol='transparent',\n\talpha=0.5,\n\tlabel.col='black',\n\tcex=2,\n\tlwd=0,\n\tfontfamily='serif',\n\tfontface='bold',\n\tcat.col = c('red', 'blue'),\n\tcat.cex=2,\n\tcat.fontfamily='serif',\n\tcat.fontface='bold')\n")
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23 else:
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24 for i in range(6):
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25 counts[i+1] = counts[i+1]+counts[i]
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26 rscript.write("venn =venn.diagram(\n\tx=list(\n\t\t"+labels[0]+"=c(1:"+str(counts[0])+","+str(counts[2]+1)+":"+str(counts[3])+","+str(counts[4]+1)+":"+str(counts[6])+"),\n\t\t"+labels[1]+"=c("+str(counts[0]+1)+":"+str(counts[1])+","+str(counts[2]+1)+":"+str(counts[4])+","+str(counts[5]+1)+":"+str(counts[6])+"),\n\t\t"+labels[2]+"=c("+str(counts[1]+1)+":"+str(counts[2])+","+str(counts[3]+1)+":"+str(counts[6])+")),\n\tfilename=NULL,\n\tfill=c('red','blue','green'),\n\tcol='transparent',\n\talpha=0.5,\n\tlabel.col='black',\n\tcex=2,\n\tlwd=0,\n\tfontfamily='serif',\n\tfontface='bold',\n\tcat.col = c('red', 'blue','green'),\n\tcat.cex=2,\n\tcat.fontfamily='serif',\n\tcat.fontface='bold')\n")
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27 rscript.write("grid.draw(venn)\n")
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28 rscript.write("dev.off()\n")
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29 rscript.close()
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30 os.system("cat "+"${script}"+" | R --vanilla --slave")
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31 </configfile>
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32 </configfiles>
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33
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34 <outputs>
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35 <data format="txt" name="script" label="${tool.name} on ${on_string}: (script)" />
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36 <data format="pdf" name="output" label="${tool.name} on ${on_string}: (plot)" />
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37
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38 </outputs>
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39
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40 <help>
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41 .. class:: infomark
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42
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43 This is a wrapper for R package VennDiagram. It allows you to plot two-set or three-set venn diagrams based on counts. The R script used to generate the plot is also in the output.
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44
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45 Input: labels for sets and counts for each region in the diagram.
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46
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47 A: A-only
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48
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49 B: B-only
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50
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51 C: C-only
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52
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53 AB: in A and B but not C
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54
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55 BC: in B and C but not A
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56
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57 AC: in A and C but not B
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58
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59 ABC: in A, B, and C
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60
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61 -----
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62
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63 **Example**
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64
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65 Labels: X,Y
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66
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67 Counts: 30,10,20
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68
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69
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70 .. image:: ./static/images/venn2.png
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71
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72
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73 Labels: A,B,C
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74
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75 Counts: 10,20,30,40,50,60,70
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76
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77
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78 .. image:: ./static/images/venn3.png
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79
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80
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81 </help>
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82 </tool>
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