diff sortmerna.xml @ 5:cd8c76234b0c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5

--- a/sortmerna.xml	Thu May 11 10:28:11 2017 -0400
+++ b/sortmerna.xml	Wed May 31 14:55:32 2017 -0400
@@ -1,7 +1,10 @@
-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.2">
+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.3">
     <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="2.1b">sortmerna</requirement>
+        <requirement type="package" version="@VERSION@">sortmerna</requirement>
     </requirements>
     <stdio>
         <regex match="This program builds a Burst trie on an input rRNA database"
@@ -33,16 +36,16 @@
         #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])
+        #set $data_table = dict([(_[0], _[3]) 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] + ',' + $os.path.splitext($data_table[$db])[0] + '-reindexed'
+            #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], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
+        #set $data_table = dict([(_[0], _[3]) 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] + ',' + $os.path.splitext($data_table[$db])[0]
+            #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db]
             #set $sep = ':'
         #end for
     #end if