# HG changeset patch
# User davidvanzessen
# Date 1438692734 14400
# Node ID 4b997f68d769e71c2606c0caf6056c5a6acdd756
# Parent  ac5794b9d300e04ef2e10dbad53aff265d223f60
Uploaded

diff -r ac5794b9d300 -r 4b997f68d769 merge_and_filter.r
--- a/merge_and_filter.r	Thu Jun 25 05:38:55 2015 -0400
+++ b/merge_and_filter.r	Tue Aug 04 08:52:14 2015 -0400
@@ -31,10 +31,14 @@
 
 summ = merge(summ, gene_identification, by="Sequence.ID")
 
-if(functionality == "no_results"){
-	summ = summ[summ$Functionality != "No results",]
-} else if (functionality == "no_result_unproductive"){
-	summ = summ[summ$Functionality != "No results" & summ$Functionality != "unproductive",]
+summ = summ[summ$Functionality != "No results",]
+
+if(functionality == "productive"){
+	summ = summ[summ$Functionality == "productive (see comment)" | summ$Functionality == "productive",]
+} else if (functionality == "unproductive"){
+	summ = summ[summ$Functionality == "unproductive (see comment)" | summ$Functionality == "unproductive",]
+} else if (functionality == "remove_no_result"){
+	summ = summ[summ$Functionality != "No results" & summ$Functionality != "unknown (see comment)" & summ$Functionality != "unknown",]
 }
 
 higher_than=(summ$chunk_hit_percentage >= 70 & summ$nt_hit_percentage >= 70)
diff -r ac5794b9d300 -r 4b997f68d769 mutation_analysis.xml
--- a/mutation_analysis.xml	Thu Jun 25 05:38:55 2015 -0400
+++ b/mutation_analysis.xml	Tue Aug 04 08:52:14 2015 -0400
@@ -14,9 +14,10 @@
 			<option value="no" selected="true">no</option>
 		</param>
 		<param name="functionality" type="select" label="Functionality filter" help="" >
-			<option value="no_results" selected="true">Remove "No results"</option>
-			<option value="no_result_unproductive">Remove "No results" and "unproductive"</option>
-			<option value="dont_remove">Don't filter</option>
+			<option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option>
+			<option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option>
+			<option value="remove_no_result">Remove "No Results", "unknown" and "unknown (see comment)"</option>
+			<option value="dont_filter">Don't filter</option>
 		</param>
 		
 		<param name="unique" type="select" label="Remove duplicates based on" help="" >
diff -r ac5794b9d300 -r 4b997f68d769 wrapper.sh