# HG changeset patch
# User bebatut
# Date 1488541869 18000
# Node ID 56e8ce2f3c96daebd5356e9827184e716b0a10b3
# Parent  8b86d590b4428c67f817c865da88936f671fb752
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f45f31529390153bdaf93a3c94a65f6888ed484b\n'-dirty

diff -r 8b86d590b442 -r 56e8ce2f3c96 README.rst
--- a/README.rst	Fri Mar 03 06:40:48 2017 -0500
+++ b/README.rst	Fri Mar 03 06:51:09 2017 -0500
@@ -4,11 +4,9 @@
 Galaxy should be able to automatically install the dependencies, i.e. the
 HUMAnN2 binaries and its dependencies.
 
-After installation, you must tell Galaxy about the defaut database with
-clade-specific marker genes used for taxonomic profiling (MetaPhlAn2), and where
-to find it:
+After installation, you must tell Galaxy about the defaut databases for MetaPhlAn2 and HUMAnN2. 
+You need to use the data managers for that and installing:
 
-* Put the ``metaphlan2_db.loc`` file in the ``tool-data/`` folder, after uncommenting last line
-* Download whole MetaPhlan2 source code: https://bitbucket.org/biobakery/metaphlan2/get/2.5.0.zip
-* Unzip it
-* Move ``db_v20`` folder into ``dependency_dir/metaphlan2/2.5.0/bebatut/package_metaphlan2_2_5_0/...`` folder
+- MetaPhlAn2 database
+- HUMAnN2 nucleotide database
+- HUMAnN2 protein database
\ No newline at end of file
diff -r 8b86d590b442 -r 56e8ce2f3c96 humann2.xml
--- a/humann2.xml	Fri Mar 03 06:40:48 2017 -0500
+++ b/humann2.xml	Fri Mar 03 06:51:09 2017 -0500
@@ -59,21 +59,21 @@
             $bypass_nucleotide_search
             --annotation-gene-index $annotation_gene_index
 
-            #set $metaphlan_option = '-t rel_ab'
+            #set $metaphlan_option = "-t rel_ab"
             #if $taxo_profile.taxonomic_profile_test == "true":
                 --taxonomic-profile '$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
-                    #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='$metaphlan_option'
+            --metaphlan-options="$metaphlan_option"
 
             #if $nucleotide_db.nucleotide_db_selector == "cached"
                 --nucleotide-database '$nucleotide_db.nucleotide_database.fields.path'