--- a/imgt_concatenate.xml	Mon Aug 29 05:46:28 2016 -0400
+++ b/imgt_concatenate.xml	Thu Nov 24 10:27:14 2016 -0500
@@ -2,16 +2,40 @@
 	<description> </description>
 	<command interpreter="bash">
 		imgt_concatenate.sh $out_file 
-#for $i, $f in enumerate($files)
- "$f.file"
-#end for
+#if str( $with_id.with_id_selector ) == "true":
+	#for $i, $f in enumerate($with_id.files)
+	 "$f.file"
+	 "$f.id"
+	#end for
+#else
+	#for $i, $f in enumerate($with_id.files)
+	 "$f.file"
+	 ""
+	#end for
+#end if
 	</command>
 	<inputs>
-		<repeat name="files" title="Sample" min="2" default="2">
-			<param name="file" format="peptideshaker_archive" type="data" label="IMGT zip file" />
-		</repeat>
+		<conditional name="with_id">
+			<param name="with_id_selector" type="select" label="Add a file ID to the sequence ID">
+				<option value="true">Add file ID to SequenceID to identify the origin file</option>
+				<option value="false" selected="True">Keep SequenceID as is</option>
+			</param>
+			<when value='true'>
+				<repeat name="files" title="Sample" min="2" default="2">
+					<param name="file" format="peptideshaker_archive" type="data" label="IMGT zip file" />
+					<param name="id" type="text" label="ID for dataset" size="25">
+						<validator type="regex" message="Fill in an ID">.+</validator>
+					</param>
+				</repeat>
+			</when>
+			<when value='false'>
+				<repeat name="files" title="Sample" min="2" default="2">
+					<param name="file" format="peptideshaker_archive" type="data" label="IMGT zip file" />
+				</repeat>
+			</when>
+		</conditional>
 		<param name="label" type="text" label="A name for the new dataset" size="25">
-			<validator type="length" message="Fill in a name for the new dataset" min="1" />
+			<validator type="regex" message="Fill in a name for the new dataset">.+</validator>
 		</param>
 	</inputs>
 	<outputs>