# HG changeset patch
# User stef
# Date 1425567219 18000
# Node ID 05e5358b8828a63ab4f29dd21ae7cc5865747eee
# Parent  81ba2f857fe259b3908a6645f6a3024e7c008f45
Uploaded

diff -r 81ba2f857fe2 -r 05e5358b8828 QDNAseq.R
--- a/QDNAseq.R	Wed Mar 04 08:42:14 2015 -0500
+++ b/QDNAseq.R	Thu Mar 05 09:53:39 2015 -0500
@@ -290,7 +290,7 @@
 
 	## proceed with segmenting / calling if requested
 	if ( doSegment ){
-		copyNumbersSegmented  <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD, transformFun="sqrt" )
+		copyNumbersSegmented  <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD, transformFun=c("sqrt") )
 		copyNumbersSegmented  <- normalizeSegmentedBins( copyNumbersSegmented )
 		outputData <- copyNumbersSegmented
 		outputType <- 'segments'
diff -r 81ba2f857fe2 -r 05e5358b8828 QDNAseq.xml
--- a/QDNAseq.xml	Wed Mar 04 08:42:14 2015 -0500
+++ b/QDNAseq.xml	Thu Mar 05 09:53:39 2015 -0500
@@ -274,22 +274,22 @@
     <!-- WHY does there seem to be no way to use split() within this code in galaxy!!! -->
     <!-- now have to fall back to using unique names within binSizes instead of just integers -->
     <!-- Problem with integers is that both "1" and "5" are also present in eg "15,100" -->
-    <data format="tsv" name="txt_1000" label="QDNAseq: ${jobName} txt 1000kb">
+    <data format="tabular" name="txt_1000" label="QDNAseq: ${jobName} txt 1000kb">
       <filter>( "bin1000kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_100" label="QDNAseq: ${jobName} txt 100kb">
+    <data format="tabular" name="txt_100" label="QDNAseq: ${jobName} txt 100kb">
       <filter>("bin100kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_30" label="QDNAseq: ${jobName} txt 30kb">
+    <data format="tabular" name="txt_30" label="QDNAseq: ${jobName} txt 30kb">
       <filter>("bin30kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_15" label="QDNAseq: ${jobName} txt 15kb">
+    <data format="tabular" name="txt_15" label="QDNAseq: ${jobName} txt 15kb">
       <filter>("bin15kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_5" label="QDNAseq: ${jobName} txt 5kb">
+    <data format="tabular" name="txt_5" label="QDNAseq: ${jobName} txt 5kb">
       <filter>("bin5kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
-    <data format="tsv" name="txt_1" label="QDNAseq: ${jobName} txt 1kb">
+    <data format="tabular" name="txt_1" label="QDNAseq: ${jobName} txt 1kb">
       <filter>("bin1kb" in binSizes and txt2history == 'TRUE')</filter>
     </data>
 
@@ -356,7 +356,7 @@
 
 .. class:: warningmark
 
-Requires **internet access** for downloading bin-annotations from bitbucket and to show some styling (css) of the final report
+Some optional history input/output files are of format "rds" (file format to store a R object). This is not registered in galaxy by default, so has to be added to the available datatypes.
 
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