# HG changeset patch
# User davidvanzessen
# Date 1406124785 14400
# Node ID aa4b95abef111bfbaf285d7396535ced7582c0c9
# Parent  be17e1e7dc2bf7091526878dcbf8acc083cad77c
Uploaded

diff -r be17e1e7dc2b -r aa4b95abef11 baseline_generator.xml
--- a/baseline_generator.xml	Wed Jul 23 07:51:10 2014 -0400
+++ b/baseline_generator.xml	Wed Jul 23 10:13:05 2014 -0400
@@ -4,7 +4,7 @@
 		wrapper.sh $in_file $reference $out_file
 	</command>
 	<inputs>
-		<param name="in_file" type="data" label="Input excel file" />
+		<param name="in_file" type="data" label="Input excel or IMGT zip file" />
 		<param name="reference" type="data" format="fasta" label="Reference fasta file" />
 	</inputs>
 	<outputs>
diff -r be17e1e7dc2b -r aa4b95abef11 script_imgt.py
--- a/script_imgt.py	Wed Jul 23 07:51:10 2014 -0400
+++ b/script_imgt.py	Wed Jul 23 10:13:05 2014 -0400
@@ -54,7 +54,7 @@
 		for line in i.readlines()[1:]:
 			linesplt = line.split("\t")
 			ref = filterGene(linesplt[1], vPattern)
-			if not ref:
+			if not ref or not linesplt[2].rstrip():
 				continue
 			if ref in outputdic:
 				outputdic[ref] += [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]