# HG changeset patch
# User yating-l
# Date 1494618759 14400
# Node ID 275949b792a4729d2e3382f1073fa9548f62d7b9
# Parent  401304052f2f3be03f4251c4c31bb919ab8e990c
planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty

diff -r 401304052f2f -r 275949b792a4 blat.xml
--- a/blat.xml	Fri May 12 15:20:23 2017 -0400
+++ b/blat.xml	Fri May 12 15:52:39 2017 -0400
@@ -5,14 +5,20 @@
       <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-    blat 
+    #set $reference_fasta_filename = "localref.fa"
+        #if str($reference_source.reference_source_selector) == "history":
+            ln -s '${reference_source.database}' '${reference_fasta_filename}'
+        #else:
+            #set $reference_fasta_filename = str($reference_source.database.fields.path)
+        #end if
+    && blat 
         #if $noHead == "yes"
           -noHead
         #end if
         -q=$query_type
         -t=$database_type
         -mask=$mask
-        '${database}'
+        '${reference_fasta_filename}'
         '${query}'
         output
     && sort -k 10,10 -k 12,12n output > '${output_sorted}'