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