# HG changeset patch
# User stef
# Date 1409053120 14400
# Node ID 2d939f4c23feb64116188066f45eb1d776971ae8
# Parent  823791a3d7e12e2dd2fcc4784afabb97c0bb63f4
Uploaded

diff -r 823791a3d7e1 -r 2d939f4c23fe LGG150_calls_example.png
Binary file LGG150_calls_example.png has changed
diff -r 823791a3d7e1 -r 2d939f4c23fe LGG150_copynumber_example.png
Binary file LGG150_copynumber_example.png has changed
diff -r 823791a3d7e1 -r 2d939f4c23fe QDNAseq.R
--- a/QDNAseq.R	Wed Aug 20 11:22:43 2014 -0400
+++ b/QDNAseq.R	Tue Aug 26 07:38:40 2014 -0400
@@ -135,7 +135,7 @@
 ## ==================================================
 MAIN_NAME <- '[INFO] '
 TOOL_PATH <- getScriptPath()
-CSS_FILE  <- paste( TOOL_PATH, '/QDNAseq.css', sep="" )
+CSS_FILE  <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
 DECIMALS  <- 3
 WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
 PURE_CSS  <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
@@ -299,7 +299,7 @@
 		png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
 			par( PAR_SET )
 			plot( copyNumbersSmooth[ ,sample ], main=paste(sample, ": CopyNumbers", sep="") ); 
-			mtext( paste( "(", binSizeString, " bins)", sep=""), 3 )
+			mtext( paste( "(", binSizeString, " bins)" sep=""), 3 )
 			abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
 		dev.off()
 		
@@ -314,7 +314,7 @@
 			png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
 				par( PAR_SET )
 				plot( copyNumbersSegmented[ ,sample ], main=paste(sample, ": CopyNumbers and Segments", sep="") ); 
-				mtext( paste( "(", binSizeString, " bins)", sep=""), 3 )
+				mtext( paste( "(", binSizeString, " bins)" sep=""), 3 )
 				abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
 			dev.off()
 
diff -r 823791a3d7e1 -r 2d939f4c23fe QDNAseq.css
--- a/QDNAseq.css	Wed Aug 20 11:22:43 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-/* --- QDNAseq CSS --- */
-body{ padding: 0px 20px; }
-pre { padding: 0px 25px; }
-h3.qdnaseq{ color: #355681;	border-bottom: 1px solid #355681;}
-.marker { background: yellow; color: red;}
-.button { background: rgb(28, 184, 65); color: white; border-radius: 4px; padding: 4px 10px }
diff -r 823791a3d7e1 -r 2d939f4c23fe QDNAseq.xml
--- a/QDNAseq.xml	Wed Aug 20 11:22:43 2014 -0400
+++ b/QDNAseq.xml	Tue Aug 26 07:38:40 2014 -0400
@@ -6,14 +6,13 @@
     <!-- <requirement type="package" version="3.1.0">R</requirement> -->
     <!-- <requirement type="package" version="1.0.5">qdnaseq</requirement> -->
     <requirement type="package" version="0.1.18">samtools</requirement>
-    <requirement type="set_environment">TOOL_DIR</requirement>
   </requirements>
 
   <description>Quantitative copy number abberation detection</description>
 
   <!-- command block to call script with default R installation -->
   <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) -->
-  <command interpreter="Rscript"> 
+  <command interpreter="/ccagc/lib/R/R-3.1.0/bin/Rscript"> 
     QDNAseq.R 
     $qdnaseq_cfg
   </command>
@@ -55,7 +54,7 @@
     <!-- ==================== -->
     <!-- Input BAMs -->
     <!-- ==================== -->
-    <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select the BAM files to analyze" />
+    <param name="bams" type="data" multiple="true" optional="True" format="bam" label="Input BAMs" help="Select the BAM files to analyze" />
 
     <!-- ==================== -->
     <!-- Optional segmenting -->
@@ -284,7 +283,7 @@
 
 .. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
 
-.. image:: ./LGG150_copynumber_example.png :height: 240 :width: 480
+.. image:: LGG150_copynumber_example.png :height: 240 :width: 480
 
   </help>
 
diff -r 823791a3d7e1 -r 2d939f4c23fe static/css/QDNAseq.css
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/css/QDNAseq.css	Tue Aug 26 07:38:40 2014 -0400
@@ -0,0 +1,6 @@
+/* --- QDNAseq CSS --- */
+body{ padding: 0px 20px; }
+pre { padding: 0px 25px; }
+h3.qdnaseq{ color: #355681;	border-bottom: 1px solid #355681;}
+.marker { background: yellow; color: red;}
+.button { background: rgb(28, 184, 65); color: white; border-radius: 4px; padding: 4px 10px }
diff -r 823791a3d7e1 -r 2d939f4c23fe static/images/LGG150_copynumber_example.png
Binary file static/images/LGG150_copynumber_example.png has changed