# HG changeset patch
# User rnateam
# Date 1497364855 14400
# Node ID 035f14f54ba75062612600f4a1e61dcd0e7b55af
# Parent  5dea7dfae0390950ea494b3f6a9559b1f4e24d6c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55

diff -r 5dea7dfae039 -r 035f14f54ba7 sortmerna.xml
--- a/sortmerna.xml	Tue Jun 06 13:43:13 2017 -0400
+++ b/sortmerna.xml	Tue Jun 13 10:40:55 2017 -0400
@@ -35,17 +35,13 @@
             #set $sep = ':'
         #end for
     #else if str( $databases_type.databases_selector ) == 'cached_to_index'
-        ## databases path is not directly accessible, must match by hand with LOC file contents
-        #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
-        #for $db in $databases_type.input_databases.value
-            #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] + '-reindexed'
+        #for $db in $databases_type.input_databases.fields.path.split(",")
+            #set $ref += $sep + $db + ',' + $os.path.splitext($db)[0] + '-reindexed'
             #set $sep = ':'
         #end for
-    #else:
-        ## databases path is not directly accessible, must match by hand with LOC file contents
-        #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
-        #for $db in $databases_type.input_databases.value
-            #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db]
+    #else
+        #for $db in $databases_type.input_databases.fields.path.split(",")
+            #set $ref += $sep + $db + ',' + $os.path.splitext($db)[0]
             #set $sep = ':'
         #end for
     #end if