Mercurial > repos > xuebing > sharplab_seq_motif
view mytools/genomeView.xml @ 0:39217fa39ff2
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author | xuebing |
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date | Tue, 13 Mar 2012 23:34:52 -0400 |
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<tool id="genomeview" name="whole genome"> <description>plot and correlation</description> <command>cat $script_file | R --vanilla --slave 2> err.log </command> <inputs> <param name="genome" type="select" label="Select genome"> <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option> <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option> <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option> <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option> </param> <param name="resolution" type="integer" label="resolution" value="5000" help="resolution in bps. It must be between 200 and 10,000,000"> <validator type="in_range" max="1000000000" min="200" message="Resolution is out of range, Resolution has to be between 200 to 100000000" /> </param> <param name="log" label="plot the log" type="boolean" truevalue="log" falsevalue="none" checked="False"/> <param name="union" label="compute correlation in union regions" help="ignore regions covered by neither interval sets. Recommended for sparse data under high resolution when most regions are empty" type="boolean" truevalue="union" falsevalue="none" checked="False"/> <repeat name="series" title="input file"> <param name="label" type="text" value="" size="30" label="Data Label"/> <param name="input" type="data" format="interval" label="Dataset"/> </repeat> </inputs> <configfiles> <configfile name="script_file"> ## Setup R error handling to go to stderr options(warn=-1) source("/Users/xuebing/galaxy-dist/tools/mytools/genomeview.r") genome = read.table( "${genome}") uselog = as.character("${log}") union = as.character("${union}") resolution = as.integer("${resolution}") cat('resolution=',resolution,'\n') offset = caloffset(genome) mcov = matrix(ncol=1,nrow=as.integer(offset[length(offset)] / resolution)) ## Open output PDF file pdf( "${out_file1}" ,height=4,width=20) labels = character(0) ## Determine range of all series in the plot #for $i, $s in enumerate( $series ) x = read.table( "${s.input.file_name}" ) res = coverage(x,genome,offset,resolution) plotcov(res,genome,offset,"${s.label.value}",uselog) labels = c(labels,"${s.label.value}") attach(res) mcov = cbind(mcov,cov) detach(res) #end for dev.off() pdf("${out_file2}") mcov = mcov[,-1] nSample = length(labels) if (nSample > 1) { if (union == 'union') { cm = matrix(0,nrow=nSample,ncol=nSample) for (i in 1:(nSample-1)) { cm[i,i] = 1 for (j in (i+1):nSample){ cm[i,j] = union_correlation(mcov[,i],mcov[,j]) cm[j,i] = cm[i,j] } } cm[nSample,nSample] = 1 } else { cm = cor(mcov) } rm(mcov) ##heatmap(-cm,margins=c(8,8),sym=T,scale='none',labRow=labels,labCol=labels) ##heatmap2(cm,'none',TRUE,c(8,8),labels,labels) x = cm h = heatmap(-x,scale='none',sym=T,margins=c(8,8),labRow=labels,labRol=labels) attach(h) x = x[rowInd,colInd] tx = numeric(0) ty = numeric(0) txt = character(0) for (i in 1:nrow(x)){ for (j in 1:ncol(x)){ tx = c(tx,i) ty = c(ty,ncol(x)-j+1) txt = c(txt,round(x[i,j]*100)/100) } } heatmap(-x,scale='none',sym=T,margins=c(8,8),labRow=labels[rowInd],labCol=labels[colInd],add.expr=text(tx,ty,txt,col='black')) library(gplots) heatmap.2(cm,margins=c(8,8),scale='none',key=TRUE,trace='none', symkey=T,symbreaks=T,col=bluered,labRow=labels,labCol=labels,symm=T) } dev.off() </configfile> </configfiles> <outputs> <data format="pdf" name="out_file1" label="${tool.name} on ${on_string}: (plot)" /> <data format="pdf" name="out_file2" label="${tool.name} on ${on_string}: (correlation)" /> </outputs> <help> .. class:: infomark 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. ----- **Example** .. image:: ./static/images/correlationmatrix.png .. image:: ./static/images/wholegenome.png </help> </tool>