# HG changeset patch
# User davidvanzessen
# Date 1458141535 14400
# Node ID 79696e273853a1c9268a0f6be30ab8ca407c9f54
# Parent  8bb4d6009e08ca5006799a8455a81faa1996d5f2
Uploaded

diff -r 8bb4d6009e08 -r 79696e273853 aa_histogram.r
diff -r 8bb4d6009e08 -r 79696e273853 merge_and_filter.r
--- a/merge_and_filter.r	Tue Mar 01 06:53:40 2016 -0500
+++ b/merge_and_filter.r	Wed Mar 16 11:18:55 2016 -0400
@@ -12,7 +12,7 @@
 method=args[9]
 functionality=args[10]
 unique_type=args[11]
-filter_unique=args[12] == "yes"
+filter_unique=args[12]
 
 summ = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
 sequences = read.table(sequencesfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
@@ -92,8 +92,7 @@
 
 print(paste("filter uniques: ", filter_unique))
 
-if(filter_unique){
-	
+if(filter_unique != "no"){
 	clmns = names(result)
 	
 	result$unique.def = paste(result$CDR1.Seq, result$CDR2.Seq, result$CDR3.Seq, result$FR1.IMGT, result$FR2.IMGT, result$FR3.IMGT)
@@ -104,6 +103,10 @@
 	
 	result = result[fltr,]
 	
+	if(filter_unique == "keep"){
+		result = result.removed
+	}
+	
 	result = result[,clmns]
 	
 	#write.table(inputdata.removed, "unique_removed.csv", sep=",",quote=F,row.names=F,col.names=T)
diff -r 8bb4d6009e08 -r 79696e273853 mutation_analysis.xml
--- a/mutation_analysis.xml	Tue Mar 01 06:53:40 2016 -0500
+++ b/mutation_analysis.xml	Wed Mar 16 11:18:55 2016 -0400
@@ -36,6 +36,7 @@
 		<param name="filter_uniques" type="select" label="Filter unique sequences" help="Filter out the sequences (based on CDR1, FR2, CDR2, FR3 and CDR3) that only occur once.">
 			<option value="yes">Yes</option>
 			<option value="no" selected="true">No</option>
+			<option value="keep">Keep uniques and filter out the duplicates</option>
 		</param>
 	</inputs>
 	<outputs>
diff -r 8bb4d6009e08 -r 79696e273853 wrapper.sh