# HG changeset patch
# User bebatut
# Date 1488541010 18000
# Node ID a8d89b78b6e2bf32788e4badc02fe4ce0075e420
# Parent  8192fbe69c0e460c0270ca9f8772fd15dc90ec21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f45f31529390153bdaf93a3c94a65f6888ed484b\n'-dirty

diff -r 8192fbe69c0e -r a8d89b78b6e2 humann2.xml
--- a/humann2.xml	Fri Mar 03 06:18:29 2017 -0500
+++ b/humann2.xml	Fri Mar 03 06:36:50 2017 -0500
@@ -64,13 +64,13 @@
                 --taxonomic-profile '$taxo_profile.taxonomic_profile'
             #else
                 #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
-                    #set $metaphlan_option += " --bowtie2db " + ref_db/ref_db
-                    #set $metaphlan_option += " --mpa_pkl " + ref_db/metadata.pkl
+                    #set $metaphlan_option += ' --bowtie2db ' + ref_db/ref_db
+                    #set $metaphlan_option += ' --mpa_pkl ' + ref_db/metadata.pkl
                 #else
                     #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path
                     #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value
-                    --bowtie2db $path/$value
-                    --mpa_pkl $path/$value'.pkl'
+                    #set $metaphlan_option += ' --bowtie2db ' + $path/$value
+                    #set $metaphlan_option += ' --mpa_pkl ' + $path/$value + '.pkl'
                 #end if
             #end if
             --metaphlan-options="$metaphlan_option"