# HG changeset patch
# User bebatut
# Date 1488542638 18000
# Node ID 928ad2c3e0c2938c9de4e9ccd678ca17da6cf46d
# Parent  56e8ce2f3c96daebd5356e9827184e716b0a10b3
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f45f31529390153bdaf93a3c94a65f6888ed484b\n'-dirty

diff -r 56e8ce2f3c96 -r 928ad2c3e0c2 humann2.xml
--- a/humann2.xml	Fri Mar 03 06:51:09 2017 -0500
+++ b/humann2.xml	Fri Mar 03 07:03:58 2017 -0500
@@ -44,7 +44,7 @@
                 bowtie2-build '$taxo_profile.metaphlan2_db_choice.metaphlan2_db_sequences ref_db/ref_db'
                 &&
                 python '$__tool_directory__/transform_json_to_pkl.py'
-                    --json_input '$metaphlan2_db_metadata'
+                    --json_input '$taxo_profile.metaphlan2_db_choice.metaphlan2_db_metadata'
                     --pkl_output 'ref_db/metadata.pkl'
                 &&
             #end if
@@ -69,8 +69,8 @@
                 #else
                     #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path
                     #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value
-                    #set $metaphlan_option += " --bowtie2db " + $path/$value
-                    #set $metaphlan_option += " --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"