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11
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1 <tool id="genomeview" name="whole genome">
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2 <description>plot and correlation</description>
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3 <command>cat $script_file | R --vanilla --slave 2> err.log </command>
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4 <inputs>
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5 <param name="genome" type="select" label="Select genome">
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6 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
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7 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
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8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
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9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
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10 </param>
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11 <param name="resolution" type="integer" label="resolution" value="5000" help="resolution in bps. It must be between 200 and 10,000,000">
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12 <validator type="in_range" max="1000000000" min="200" message="Resolution is out of range, Resolution has to be between 200 to 100000000" />
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13 </param>
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14 <param name="log" label="plot the log" type="boolean" truevalue="log" falsevalue="none" checked="False"/>
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15 <param name="union" label="compute correlation in union regions" help="ignore regions covered by neither interval sets. Recommended for sparse data under high resolution when most regions are empty" type="boolean" truevalue="union" falsevalue="none" checked="False"/>
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16 <repeat name="series" title="input file">
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17 <param name="label" type="text" value="" size="30" label="Data Label"/>
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18 <param name="input" type="data" format="interval" label="Dataset"/>
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19 </repeat>
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20 </inputs>
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21
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22 <configfiles>
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23 <configfile name="script_file">
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24 ## Setup R error handling to go to stderr
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25 options(warn=-1)
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26 source("/Users/xuebing/galaxy-dist/tools/mytools/genomeview.r")
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27 genome = read.table( "${genome}")
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28 uselog = as.character("${log}")
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29 union = as.character("${union}")
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30 resolution = as.integer("${resolution}")
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31 cat('resolution=',resolution,'\n')
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32 offset = caloffset(genome)
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33 mcov = matrix(ncol=1,nrow=as.integer(offset[length(offset)] / resolution))
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34 ## Open output PDF file
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35 pdf( "${out_file1}" ,height=4,width=20)
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36 labels = character(0)
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37 ## Determine range of all series in the plot
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38 #for $i, $s in enumerate( $series )
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39 x = read.table( "${s.input.file_name}" )
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40 res = coverage(x,genome,offset,resolution)
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41 plotcov(res,genome,offset,"${s.label.value}",uselog)
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42 labels = c(labels,"${s.label.value}")
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43 attach(res)
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44 mcov = cbind(mcov,cov)
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45 detach(res)
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46 #end for
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47 dev.off()
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48 pdf("${out_file2}")
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49 mcov = mcov[,-1]
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50 nSample = length(labels)
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51 if (nSample > 1) {
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52 if (union == 'union') {
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53 cm = matrix(0,nrow=nSample,ncol=nSample)
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54 for (i in 1:(nSample-1)) {
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55 cm[i,i] = 1
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56 for (j in (i+1):nSample){
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57 cm[i,j] = union_correlation(mcov[,i],mcov[,j])
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58 cm[j,i] = cm[i,j]
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59 }
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60 }
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61 cm[nSample,nSample] = 1
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62 } else {
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63 cm = cor(mcov)
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64 }
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65 rm(mcov)
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66 ##heatmap(-cm,margins=c(8,8),sym=T,scale='none',labRow=labels,labCol=labels)
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67 ##heatmap2(cm,'none',TRUE,c(8,8),labels,labels)
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68 x = cm
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69 h = heatmap(-x,scale='none',sym=T,margins=c(8,8),labRow=labels,labRol=labels)
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70 attach(h)
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71 x = x[rowInd,colInd]
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72 tx = numeric(0)
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73 ty = numeric(0)
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74 txt = character(0)
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75 for (i in 1:nrow(x)){
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76 for (j in 1:ncol(x)){
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77 tx = c(tx,i)
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78 ty = c(ty,ncol(x)-j+1)
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79 txt = c(txt,round(x[i,j]*100)/100)
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80 }
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81 }
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82 heatmap(-x,scale='none',sym=T,margins=c(8,8),labRow=labels[rowInd],labCol=labels[colInd],add.expr=text(tx,ty,txt,col='black'))
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83 library(gplots)
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84 heatmap.2(cm,margins=c(8,8),scale='none',key=TRUE,trace='none', symkey=T,symbreaks=T,col=bluered,labRow=labels,labCol=labels,symm=T)
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85 }
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86 dev.off()
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87 </configfile>
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88 </configfiles>
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89
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90 <outputs>
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91 <data format="pdf" name="out_file1" label="${tool.name} on ${on_string}: (plot)" />
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92 <data format="pdf" name="out_file2" label="${tool.name} on ${on_string}: (correlation)" />
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93 </outputs>
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94
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95 <help>
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96 .. class:: infomark
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97
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98 This tool allows you to plot multiple intervals across all chromosomes at different resolution, and it also plots the correlation matrix if multiple intervals are provided.
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99
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100 -----
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101
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102 **Example**
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103
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104 .. image:: ./static/images/correlationmatrix.png
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105 .. image:: ./static/images/wholegenome.png
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106
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107 </help>
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108 </tool>
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