--- a/genomeView.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-<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>