--- a/mutation_analysis.xml	Thu Aug 04 04:52:51 2016 -0400
+++ b/mutation_analysis.xml	Tue Aug 09 07:20:41 2016 -0400
@@ -1,7 +1,7 @@
 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0">
 	<description></description>
 	<command interpreter="bash">
-		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter $empty_region_filter
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -28,19 +28,24 @@
 		</param>
 		<param name="unique" type="select" label="Remove duplicates based on" help="" >
 			<option value="AA.JUNCTION_V_subclass" selected="true">Top.V.Gene, CDR3.Seq, C region</option>
-			<option value="AA.JUNCTION_subclass">CDR3.Seq + C region</option>
-			<option value="AA.JUNCTION_V">CDR3.seq + Top.V.Gene</option>
+			<option value="AA.JUNCTION_subclass">CDR3.Seq, C region</option>
+			<option value="AA.JUNCTION_V">CDR3.seq, Top.V.Gene</option>
 			<option value="AA.JUNCTION">CDR3.seq</option>
 			<option value="none">Don't remove duplicates</option>
 		</param>
 		<param name="class_filter" type="select" label="Class/Subclass filter" help="" >
 			<option value="70_70" selected="true">>70% class and >70% subclass</option>
-			<option value="60_55" selected="true">>60% class and >55% subclass</option>
+			<option value="60_55">>60% class and >55% subclass</option>
 			<option value="70_0">>70% class</option>
 			<option value="60_0">>60% class</option>
 		</param>
+		<param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
+			<option value="FR1" selected="true">FR1 : exclude empty CDR1,FR2,CDR2,FR3</option>
+			<option value="CDR1">CDR1: exclude empty FR2,CDR2,FR3</option>
+			<option value="FR2">FR2: exclude empty,CDR2,FR3</option>
+		</param>
 		<conditional name="naive_output_cond">
-			<param name="naive_output" type="select" label="Output a file for naive analysis?">
+			<param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
 				<option value="yes">Yes</option>
 				<option value="no" selected="true">No</option>
 			</param>
@@ -48,13 +53,13 @@
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
-		<data format="tabular" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
+		<data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
 		</data>
-		<data format="tabular" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
+		<data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
 		</data>
-		<data format="tabular" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
+		<data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
 		</data>
 	</outputs>