--- a/humann2.xml	Thu Mar 31 03:35:17 2016 -0400
+++ b/humann2.xml	Tue Apr 12 03:06:03 2016 -0400
@@ -36,10 +36,12 @@
             #set $db = $nucleotide_database.value
             --nucleotide-database $data_table[$db]
 
-            --metaphlan \${METAPHLAN2_DIR}/
-            --metaphlan-options "-t rel_ab"
-            --bowtie2 \${PATH}
-            --diamond \${PATH}
+            #set $mpa_pkl_table = dict([(_[0], _[2]) for _ in $mpa_pkl.input.options.tool_data_table.data])
+            #set $mpa_pkl_db = $mpa_pkl.value
+
+            #set $bowtie2_table = dict([(_[0], _[2]) for _ in $bowtie2db.input.options.tool_data_table.data])
+            #set $bowtie2_db = $bowtie2db.value
+            --metaphlan-options="-t rel_ab --mpa_pkl $mpa_pkl_table[$mpa_pkl_db] --bowtie2db $bowtie2_table[$bowtie2_db]"
 
             --threads \${GALAXY_SLOTS:-4}
 
@@ -69,6 +71,14 @@
             <when value="false" />
         </conditional>
 
+        <param name="mpa_pkl" label="Metadata for MetaPhlAn2" type="select" >
+            <options from_data_table="metaphlan2_metadata" />
+        </param>
+
+        <param name="bowtie2db" label="BowTie2 database for MetaPhlAn2" type="select" >
+            <options from_data_table="metaphlan2_bowtie_db" />
+        </param>
+
         <param name="nucleotide_database" label="Nucleotide database" type="select" >
             <options from_data_table="humann2_nucleotide_database" />
         </param>