--- a/vidjil.xml	Thu Feb 12 09:54:07 2015 -0500
+++ b/vidjil.xml	Thu Feb 12 10:47:15 2015 -0500
@@ -1,17 +1,11 @@
 <tool id="vidjil_galaxy_wrapper" name="Vidjil" version="1.0">
 	<description></description>
 	<command interpreter="bash">
-		vidjil.sh "
-#for $i, $f in enumerate($in_files)
-${f.id};${f.in_file}|
-#end for
-" $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline
+		vidjil.sh $in_file $id $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline $fasta_out
 	</command>
 	<inputs>
-		<repeat name="in_files" title="Input Files" min="1" default="1">
-			<param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
-			<param name="id" type="text" label="ID" />
-		</repeat>
+		<param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
+		<param name="id" type="text" label="ID" />
 		<param name="database" type="select" label="Database">
 			<option value="current">Germline database from IMGT of 30-9-14</option>
 			<option value="download">Download newest database from IMGT</option>
@@ -34,7 +28,8 @@
 		<param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/>
 	</inputs>
 	<outputs>
-		<data format="html" name="out_file" label="Vidjil on blah"/>
+		<data format="html" name="out_file" label="Vidjil browser of ${in_file.name}"/>
+		<data format="fasta" name="fasta_out" label="Vidjil fasta of ${in_file.name}" />
 	</outputs>
 	<help>
 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.