# HG changeset patch
# User stef
# Date 1403085234 14400
# Node ID 2517af3f347595d113d108a44e669d81a38a31eb
# Parent  647143d0c884e540eeef6f1b590272a40d22de4f
Uploaded

diff -r 647143d0c884 -r 2517af3f3475 QDNAseq.R
--- a/QDNAseq.R	Wed Jun 18 05:45:02 2014 -0400
+++ b/QDNAseq.R	Wed Jun 18 05:53:54 2014 -0400
@@ -177,8 +177,6 @@
 DECIMALS  <- 3
 WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
 
-
-
 catMsg( "Starting QDNAseq wrapper" )	
 catMsg( "Loading R libraries" )
 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
@@ -186,7 +184,7 @@
 
 systemUser <- system("whoami",T)
 qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
-catMsg( c(" Hello ", systemUser ) )
+catMsg( c("Analysis run with user: ", systemUser ) )
 catMsg( c("QDNAseq version loaded: ", qdnaseqVersion) )
 
 ## only one param: the tmp config file
@@ -286,7 +284,7 @@
 ## save objects to output dir
 saveRDS( readCounts, robjReadCoPath );
 saveRDS( copyNumbersSmooth, robjCopyNrPath );
-exportBins(copyNumbersSmooth, file=igvCopyNrName, format="igv")
+exportBins(copyNumbersSmooth, file=igvCopyNrPath, format="igv")
 
 ## also save objects for galaxy history output if requested
 if ( doOutputReadcountsRds ){
@@ -306,7 +304,7 @@
 	if ( doOutputCallsRds ){
 		saveRDS( copyNumbersCalled, calledSegmentsDatasetFile );
 	}
-	exportBins( copyNumbersCalled, file=igvCalledName, format="igv")
+	exportBins( copyNumbersCalled, file=igvCalledPath, format="igv")
 }
 
 
@@ -375,6 +373,8 @@
 copyNrSize <- paste( round( file.info( robjCopyNrPath )[["size"]] / 1000000, digits=2 ), 'MB' )
 calledSize <- paste( round( file.info( robjCalledPath )[["size"]] / 1000000, digits=2 ), 'MB' )
 regionSize <- paste( round( file.info( robjRegionPath )[["size"]] / 1000000, digits=2 ), 'MB' )
+igvCopyNrSize <- paste( round( file.info( igvCopyNrPath )[["size"]] / 1000000, digits=2 ), 'MB' )
+igvCalledSize <- paste( round( file.info( igvCallecPath )[["size"]] / 1000000, digits=2 ), 'MB' )
 
 ## ------------------------
 ## creating html output to be linked to from the middle galaxy pane
@@ -440,6 +440,9 @@
             cat( '<dd>QDNAseq object with copy numbers per bin, ', copyNrSize,'</dd>', "\n" )
             r_code <- paste( r_code, '<code class="code">copyNumbersSmooth <- readRDS(', robjCopyNrName, ")</code><br />", sep="")
             
+            cat( '<dt>', htmlLink( path=igvCopyNrName, igvCopyNrName ), '</dt>', "\n" ) 
+            cat( '<dd>IGV formatted text file with copy numbers per bin, ', igvCopyNrSize,'</dd>', "\n" )
+            
             if ( doCall ){
             	cat( '<dt>', htmlLink( path=robjCalledName, robjCalledName ), '</dt>', "\n" ) 
             	cat( '<dd>QDNAseq object with segment and call status per bin, ', calledSize,'</dd>', "\n" )
@@ -449,6 +452,9 @@
             	cat( '<dd>list with segmented/called regions for each sample, ', regionSize, '</dd>', "\n" )
             	r_code <- paste( r_code, '<code class="code">calledRegions <- readRDS(', regiOutputName, ")</code><br />", sep="")
 
+            	cat( '<dt>', htmlLink( path=igvCalledName, igvCalledName ), '</dt>', "\n" ) 
+            	cat( '<dd>IGV formatted text file with calls per bin , ', igvCalledSize,'</dd>', "\n" )
+
             }
         cat( '</dl></p>', "\n" )