--- a/vidjil.xml	Tue Dec 09 04:14:03 2014 -0500
+++ b/vidjil.xml	Thu Feb 12 09:54:07 2015 -0500
@@ -1,19 +1,40 @@
 <tool id="vidjil_galaxy_wrapper" name="Vidjil" version="1.0">
 	<description></description>
 	<command interpreter="bash">
-		vidjil.sh $in_file $out_file $out_file.files_path $database $limit_reads $limit_ratio
+		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
 	</command>
 	<inputs>
-		<param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
+		<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="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>
 		</param>
+		<param name="selection" type="select" label="Selection">
+			<option value="clones">Clones</option>
+			<option value="windows">Windows</option>
+			<option value="segment">Segment (Not recommended)</option>
+			<option value="germlines">Discover all germlines</option>
+		</param>
+		<param name="germline" type="select" label="Germline">
+			<option value="IGH">IGH</option>
+			<option value="IGK">IGK</option>
+			<option value="TRB">TRB</option>
+			<option value="IGH">IGH</option>
+			<option value="IGH">IGH</option>
+			<option value="IGH">IGH</option>
+		</param>
 		<param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/>
 		<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 ${in_file.name}"/>
+		<data format="html" name="out_file" label="Vidjil on blah"/>
 	</outputs>
 	<help>
 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.