--- a/blat.xml	Thu Jun 01 16:31:08 2017 -0400
+++ b/blat.xml	Fri Jun 23 23:33:09 2017 -0400
@@ -1,29 +1,42 @@
 <?xml version="1.0"?>
-<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
-    <description>Standalone blat sequence search command line tool</description>
+<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-0">
+    <description>BLAST-like sequence alignment tool</description>
     <requirements>
-      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
+      <requirement type="package" version="35">blat</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if str($reference_source.reference_source_selector) == "history":
-            #set $reference_fasta_filename = "localref.fa" 
+            ## blat depends on file extension
+            #if $reference_source.database.is_of_type("fasta"):
+                #set $reference_fasta_filename = "localref.fa"
+            #elif $reference_source.database.is_of_type("twobit"):
+                #set $reference_fasta_filename = "localref.2bit"
+            #else
+                #set $reference_fasta_filename = "localref"
+            #end if
+
             ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
       #else:
             #set $reference_fasta_filename = str($reference_source.database.fields.path)
       #end if
+
       blat 
             #if $noHead == "yes"
-            -noHead
+                -noHead
             #end if
+
             -q=$query_type
             -t=$database_type
+
             #if $mask_type.mask == "file.out":
-                  -mask=$mask_type.mask_file
+                  -mask='${mask_type.mask_file}'
             #else:
                   -mask=$mask_type.mask
             #end if
+
             '$reference_fasta_filename'
             '${query}'
+
             output
       && sort -k 10,10 -k 12,12n output > '${output_sorted}'
 ]]></command>
@@ -42,10 +55,10 @@
                         </param>
                   </when>
                   <when value="history">
-                        <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" />
+                        <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
                   </when>
             </conditional>
-            <param type="data" name="query" format="fasta,twobit" label="Query data, either a .fa, .nib or .2bit file"/>
+            <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
             <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">
                   <option value="dna">dna - DNA sequence</option>
                   <option value="prot">prot - protein sequence</option>
@@ -160,4 +173,4 @@
             
 
                
-    
\ No newline at end of file
+