# HG changeset patch
# User rnateam
# Date 1496770863 14400
# Node ID 185effcdfb6898741ca14209f1cdf43e07bb1ce1
# Parent  cd8c76234b0c61ce4d598a87b39b22514eeb36d2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf

diff -r cd8c76234b0c -r 185effcdfb68 sortmerna.xml
--- a/sortmerna.xml	Wed May 31 14:55:32 2017 -0400
+++ b/sortmerna.xml	Tue Jun 06 13:41:03 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.3">
+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4">
     <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
     <macros>
         <import>macros.xml</import>
@@ -36,14 +36,14 @@
         #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], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
+        #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'
             #set $sep = ':'
         #end for
     #else:
         ## databases path is not directly accessible, must match by hand with LOC file contents
-        #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
+        #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]
             #set $sep = ':'
diff -r cd8c76234b0c -r 185effcdfb68 tool-data/rRNA_databases.loc.sample
--- a/tool-data/rRNA_databases.loc.sample	Wed May 31 14:55:32 2017 -0400
+++ b/tool-data/rRNA_databases.loc.sample	Tue Jun 06 13:41:03 2017 -0400
@@ -1,1 +1,1 @@
-#<unique_id>  <database_caption>  <name>  <fasta_file_path>
+#<unique_id>  <database_caption>  <fasta_file_path>
diff -r cd8c76234b0c -r 185effcdfb68 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed May 31 14:55:32 2017 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Jun 06 13:41:03 2017 -0400
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of public ribosomal databases -->
     <table name="rRNA_databases" comment_char="#">
-        <columns>value, name, dbkey, path</columns>
+        <columns>value, name, path</columns>
         <file path="tool-data/rRNA_databases.loc" />
     </table>
 </tables>