# HG changeset patch
# User bebatut
# Date 1488539909 18000
# Node ID 8192fbe69c0e460c0270ca9f8772fd15dc90ec21
# Parent  2caada2d49bccc527abc558c5444a7e4f23d5778
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f45f31529390153bdaf93a3c94a65f6888ed484b\n'-dirty

diff -r 2caada2d49bc -r 8192fbe69c0e humann2.xml
--- a/humann2.xml	Thu Mar 02 09:25:07 2017 -0500
+++ b/humann2.xml	Fri Mar 03 06:18:29 2017 -0500
@@ -67,9 +67,10 @@
                     #set $metaphlan_option += " --bowtie2db " + ref_db/ref_db
                     #set $metaphlan_option += " --mpa_pkl " + ref_db/metadata.pkl
                 #else
-                    #set $path = $db.cached_db.fields.path
-                    --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'`
-                    --mpa_pkl `ls $path/*.pkl`
+                    #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'
                 #end if
             #end if
             --metaphlan-options="$metaphlan_option"
@@ -182,8 +183,8 @@
         </conditional>
         <param name="id_mapping" argument="--id-mapping" type="data" format="tsv" label="id mapping file for alignments" optional="True"/>
         <param name='translated_alignment' argument="--translated-alignment" type="select" label="Software to use for translated alignment" help="(--pathways)">
-            <option value="rapsearch" selected="true">Rapsearch</option>
-            <option value="diamond">Diamond</option>
+            <option value="rapsearch">Rapsearch</option>
+            <option value="diamond" selected="true">Diamond</option>
         </param>
         <param argument='--xipe' type='boolean' checked="false" truevalue='on' falsevalue='off' label="Use xipe computation?"/>
         <param argument='--minpath' type='boolean' checked="true" truevalue='on' falsevalue='off' label="Use minpath computation?"/>
diff -r 2caada2d49bc -r 8192fbe69c0e repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Mar 02 09:25:07 2017 -0500
+++ b/repository_dependencies.xml	Fri Mar 03 06:18:29 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories description="This requires the HUMAnN2 data manager definition to install all required databases.">
-    <repository changeset_revision="8602983cb86f" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="bf858d6f7365" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     <repository changeset_revision="a0eed08a6b61" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>