--- a/rapsodyn/ParseBlastForUniqueMatch.xml	Mon Sep 29 03:02:16 2014 -0400
+++ b/rapsodyn/ParseBlastForUniqueMatch.xml	Tue Oct 07 10:34:34 2014 -0400
@@ -1,16 +1,17 @@
-<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="0.01">
+<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="1.01">
 <description>Filter mpileup with blast results</description>
 <command interpreter="perl">
-    ParseBlastForUniqueMatch.pl $input_variant_file $input_blast_file $window_length $nb_mismatch_max > $output_file 
+    ParseBlastForUniqueMatch.pl -input_variant_file $input_variant_file -input_blast_file $input_blast_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max -log_file $log_file > $output_variant_file 
 </command>
 <inputs>
-<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
-<param name="input_blast_file"  type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/>
-<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
-<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
+	<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
+	<param name="input_blast_file"  type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/>
+	<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
+	<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
 </inputs>
 <outputs>
- <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="output_variant_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
 </outputs>
 
 <help>