Mercurial > repos > rnateam > sortmerna

changeset 7:1eafcc450052 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55
author rnateam
date Tue, 13 Jun 2017 10:41:34 -0400
parents 185effcdfb68
children 65c38d020fea
files sortmerna.xml
diffstat 1 files changed, 5 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/sortmerna.xml	Tue Jun 06 13:41:03 2017 -0400
+++ b/sortmerna.xml	Tue Jun 13 10:41:34 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