--- a/shm_csr.xml	Wed Jun 14 11:14:00 2017 -0400
+++ b/shm_csr.xml	Mon Jul 17 10:44:40 2017 -0400
@@ -1,5 +1,12 @@
 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0">
 	<description></description>
+	<requirements>
+		<requirement type="package" version="3.1_3">r-seqinr</requirement>
+		<requirement type="package" version="2.2.0">r-ggplot2</requirement>
+		<requirement type="package" version="1.4.2">r-reshape2</requirement>
+		<requirement type="package" version="0.4.1">r-scales</requirement>
+		<requirement type="package" version="1.10.0">r-data.table</requirement>
+	</requirements>
 	<command interpreter="bash">
 		#if str ( $filter_unique.filter_unique_select ) == "remove":
 			wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter $fast
@@ -8,7 +15,7 @@
 		#end if
 	</command>
 	<inputs>
-		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
+		<param name="in_file" type="data" format="data" label="IMGT zip file to be analysed" />
 		<param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
 			<option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
 			<option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
@@ -29,6 +36,8 @@
 			<when value="remove">
 				<param name="filter_unique_clone_count" size="4" type="integer" label="How many sequences should be in a group to keep 1 of them" value="2" min="2"/>
 			</when>
+			<when value="keep"></when>
+			<when value="no"></when>
 		</conditional>
 		<param name="unique" type="select" label="Remove duplicates based on" help="" >
 			<option value="VGene,CDR3.IMGT.AA,best_match_class">Top.V.Gene, CDR3 (AA), C region</option>
@@ -51,12 +60,20 @@
 				<option value="19_0">>19% class</option>
 				<option value="101_101">Do not assign (sub)class</option>
 			</param>
+			<when value="70_70"></when>
+			<when value="60_55"></when>
+			<when value="70_0"></when>
+			<when value="60_0"></when>
+			<when value="19_0"></when>
+			<when value="101_101"></when>
 		</conditional>
 		<conditional name="naive_output_cond">
 			<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>
+			<when value="yes"></when>
+			<when value="no"></when>
 		</conditional>
 		<param name="fast" type="select" label="Fast" help="Skips generating the new ZIP files and Change-O/Baseline" >
 			<option value="yes">Yes</option>
@@ -86,10 +103,12 @@
 		    <filter>class_filter_cond['class_filter'] == "101_101"</filter>
 		</data>
 	</outputs>
-	<citations>
-		<citation type="doi">10.1093/nar/gks457</citation>
-		<citation type="doi">10.1093/bioinformatics/btv359</citation>
-	</citations>
+	<tests>
+		<test>
+			<param name="fast" value="yes"/>
+			<output name="out_file" file="test1.html"/>
+		</test>
+	</tests>
 	<help>
 <![CDATA[
 **References**
@@ -210,4 +229,8 @@
 
 ]]>
 	</help>
+	<citations>
+		<citation type="doi">10.1093/nar/gks457</citation>
+		<citation type="doi">10.1093/bioinformatics/btv359</citation>
+	</citations>
 </tool>