--- a/metaphlan2.xml	Wed Feb 22 03:49:35 2017 -0500
+++ b/metaphlan2.xml	Wed Feb 22 09:16:03 2017 -0500
@@ -45,9 +45,9 @@
             #if $db.db_selector == "cached"
                 #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data])
                 #set $db_choice = $db.cached_db.value
-                #set $metadata = `ls $paths[$db_choice]/*.pkl`
-                --bowtie2db $metadata[:-4]
-                --mpa_pkl '$metadata'
+                metadata=`ls $paths[$db_choice]/*.pkl`
+                --bowtie2db `echo $metadata | sed 's/\(.*\)\..*/\1/'`
+                --mpa_pkl \$metadata
             #else
                 --bowtie2db 'ref_db/ref_db'
                 --mpa_pkl 'ref_db/metadata.pkl'