diff --git a/tools/metag_tools/megablast_wrapper.py b/tools/metag_tools/megablast_wrapper.py
index da1a7ef0890..44e8d5306a5 100644
--- a/tools/metag_tools/megablast_wrapper.py
+++ b/tools/metag_tools/megablast_wrapper.py
@@ -1,53 +1,15 @@
 #! /usr/bin/python
 """
 run megablast for metagenomics data
-database builds file
-usage: %prog database/reference query output
-Wen-Yu Chung
 """
 import sys, os, tempfile
 
 DB_LOC = "/depot/data2/galaxy/blastdb.loc"
 
-def print_bed_format(fields, file_handle):
-    #print " ".join(fields)
-    print >> file_handle, "\t".join(fields)
-    return 0
-
-def print_maf_format(fields, file_handle):
-    score = fields.pop(0)
-    print >> file_handle, "a score=%s" %score
-    print >> file_handle, "s %s" %" ".join(fields)
-    print >> file_handle
-    return 0
-
-def parse_megablast_output(filename, output_format, file_handle):
-    fields = []
-    file_to_be_parsed = open(filename, 'r')
-    for i, line in enumerate(file_to_be_parsed):
-        line = line.strip('\r\n')
-        if (not line.startswith("#")):
-            [query_id, subject_id, iden, align_length, mismatches, gaps, q_start, q_end, s_start, s_end, evalue, bit_score] = line.split()
-            if (int(s_start) > int(s_end)): 
-                strand = "-"
-                temp = s_start
-                s_start = s_end
-                s_end = temp
-            else:
-                strand = "+"
-            if (output_format == "bed"):
-                fields = [subject_id, s_start, s_end, query_id, str(0), strand]
-                print_bed_format(fields, file_handle)
-            else:
-                fields = [bit_score, subject_id, s_start, str(int(align_length)-int(gaps)), strand, "srcSize", "text"]
-                print_maf_format(fields, file_handle)
-    return 0
-
 def __main__():
     # file I/O
     db_build = sys.argv[1]
     query_filename = sys.argv[2]
-    #output_format = sys.argv[3]
     output_filename = sys.argv[3]
     
     # megablast parameters
@@ -63,44 +25,43 @@ def __main__():
     db = {}
     db_file = open(DB_LOC, "r")
     for i, line in enumerate(db_file):
-        line = line.strip('\r\n')
+        line = line.rstrip('\r\n')
         fields = line.split()
         db[(fields[0])] = []
         for j in xrange(1, len(fields)):
             db[(fields[0])].append(fields[j])
-    #print "\n".join(db[(db_build)])
     
     # prepare to run megablast
     if os.system('which megablast 2>&1'): print >> sys.stderr, "Cannot locate megablast."
         
     for chunk in db[(db_build)]:
-    #chunk = db[(db_build)][0]        # test
-    #if 1:                            # test
-        #if os.path.exists('/usr/bin/megablast'):
         megablast_output_file = tempfile.NamedTemporaryFile('w')
         megablast_output_filename = megablast_output_file.name   
         megablast_arguments = ["megablast", "-d", chunk, "-i", query_filename, "-o", megablast_output_filename] 
-        megablast_parameters = ["-m", "8", "-D", "3", "-a", "1"]
+        megablast_parameters = ["-m", "8", "-D", "3", "-a", "8"]
         megablast_user_inputs = ["-W", mega_word_size, "-p", mega_iden_cutoff, "-t", mega_disc_word, "-N", mega_disc_type, "-F", mega_filter]
         megablast_command = " ".join(megablast_arguments) + " " + " ".join(megablast_parameters) + " " + " ".join(megablast_user_inputs) + " 2>&1"
-        #print megablast_command
         os.system(megablast_command)
             
-        #parse_megablast_output(megablast_output_filename, output_format, output_file)
-        megablast_output_handle = open(megablast_output_filename, 'r')
-        for i, line in enumerate(megablast_output_handle):
-            line = line.strip('\r\n')
+        for i, line in enumerate( file(megablast_output_filename) ):
+            line = line.rstrip('\r\n')
             fields = line.split()
             if (not line.startswith("#")): 
                 # replace subject id with gi number
                 # remove this after re-build blastdb
                 subject_id_fields = fields[1].split('|')
-                gi = subject_id_fields[1]
+                if len(subject_id_fields) > 1: gi = subject_id_fields[1]
+                else: gi = subject_id_fields[0]
                 fields[1] = gi
                 print >> output_file, "\t".join(fields) 
-        
-        megablast_output_file.close()
     
     output_file.close()
-        
+    
+    # megablast generates a file called error.log, if empty, delete it, if not, show the contents
+    if os.path.exists('./error.log'):
+        for i, line in enumerate( file('./error.log') ):
+            line = line.rstrip('\r\n')
+            print >> sys.stdout, line
+        os.remove('./error.log')
+    
 if __name__ == "__main__" : __main__()
\ No newline at end of file
diff --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper.xml
index 9aca6b9f490..22a32c618a9 100644
--- a/tools/metag_tools/megablast_wrapper.xml
+++ b/tools/metag_tools/megablast_wrapper.xml
@@ -1,19 +1,12 @@
 <tool id="megablast_wrapper" name="Run Megablast">
-	<description>on genomic data</description>
+	<description>for Metagenomics Projects</description>
 	<command interpreter="python">megablast_wrapper.py $source_select $input_query $output1 $word_size $iden_cutoff $disc_word $disc_type $filter_query</command>
 	<inputs>
 		<param name="input_query" type="data" format="fasta" label="Query Sequence"/>
 		<param name="source_select" type="select" display="radio" label="Target database">
-			<!-- <options from_file="/depot/data2/galaxy/blastdb.loc" /> -->
 			<option value="nt">nt (for nucleotides)</option>
-		</param>
-		<!-- <param name="something" type="blastdb" label="database"/> --> 
-<!-- 
-		<param name="output_format" type="select" display="radio" label="Output Type">
-			<option value="bed">BED</option>
-			<option value="maf">MAF</option>
-		</param>
--->
+			<option value="test">Ecoli_K12</option>
+		</param> 
 		<param name="word_size" type="select" label="Word size (-W, length of best perfect match)">
 			<option value="28">28</option>
 			<option value="16">16</option>
@@ -33,12 +26,10 @@
 	<outputs>
 		<data name="output1" format="tabular"/>
 	</outputs>
-<!-- 
 	<tests>
 		<test>
 			<param name="input_query" value="megablast_query.fa" ftype="fasta"/>
-			<param name="source_select" value="nt" />
-			<param name="output_format" value="bed" />
+			<param name="source_select" value="test" />
 			<param name="word_size" value="28" />
 			<param name="iden_cutoff" value="99.0" />
 			<param name="disc_word" value="0" />
@@ -47,7 +38,6 @@
 			<output name="output1" file="megablast_test.out"/> 
 		</test>
 	</tests>
--->
 	<help>
 	
 .. class:: warningmark