diff baseline_generator.xml @ 5:048f8cdbb6d2 draft default tip

Uploaded

--- a/baseline_generator.xml	Wed Jul 23 10:13:05 2014 -0400
+++ b/baseline_generator.xml	Thu Aug 07 10:19:53 2014 -0400
@@ -1,14 +1,27 @@
 <tool id="baseline_fasta_generator" name="Baseline generator" version="1.0">
 	<description>Generate baseline fasta file</description>
 	<command interpreter="bash">
-		wrapper.sh $in_file $reference $out_file
+		wrapper.sh "
+		#for $i, $input in enumerate($inputs)
+ ${input.in_file}
+		#end for 
+		"
+		"
+		#for $i, $input in enumerate($inputs)
+ ${input.id}
+		#end for 
+		"
+    $reference $out_file
 	</command>
 	<inputs>
-		<param name="in_file" type="data" label="Input excel or IMGT zip file" />
+		<repeat name="inputs" title="inputs" min="1" default="1">
+			<param name="in_file" type="data" label="Input excel or IMGT zip file" />
+			<param name="id" type="text" label="ID (alpha-numeric, no spaces)" />
+		</repeat>
 		<param name="reference" type="data" format="fasta" label="Reference fasta file" />
 	</inputs>
 	<outputs>
-		<data format="fasta" name="out_file" label = "Baseline generator on $in_file.name with $reference.name"/>
+		<data format="fasta" name="out_file" label = "Baseline generator on ${on_string} with $reference.name"/>
 	</outputs>
 	<help>
 			Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.