--- a/shm_csr.xml	Mon Mar 27 13:11:53 2023 +0000
+++ b/shm_csr.xml	Fri Jan 05 08:53:22 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.8.1" profile="16.04">
+<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.9.0" profile="16.04">
 	<description></description>
 	<requirements>
 		<requirement type="package" version="3.7.1">python</requirement>
@@ -24,9 +24,8 @@
 		<![CDATA[
 		#import os
 		#set $input=os.path.basename($in_file.name)
-		ln -s "$in_file" "$input" &&
 		#if str ( $filter_unique.filter_unique_select ) == "remove":
-			$__tool_directory__/wrapper.sh "$input"
+			$__tool_directory__/wrapper.sh "$in_file"
 			custom $out_file $out_file.files_path
 			"$input" "-" $functionality $unique
 			$naive_output_cond.naive_output $naive_output_ca $naive_output_cg
@@ -60,6 +59,7 @@
 			<option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
 			<option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
 			<option value="FR2">FR2: include CDR2,FR3 in filters</option>
+			<option value="None">No filter: sequences with mission regions are not filtered.</option>
 		</param>
 		<param name="functionality" type="select" label="Functionality filter" help="" >
 			<option value="productive" selected="true">Productive (Productive and Productive see comment)</option>