# HG changeset patch
# User yating-l
# Date 1494624127 14400
# Node ID 355af6f61974a43f72055d4ad798e42612387e41
# Parent  275949b792a4729d2e3382f1073fa9548f62d7b9
planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty

diff -r 275949b792a4 -r 355af6f61974 blat.xml
--- a/blat.xml	Fri May 12 15:52:39 2017 -0400
+++ b/blat.xml	Fri May 12 17:22:07 2017 -0400
@@ -5,23 +5,23 @@
       <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-    #set $reference_fasta_filename = "localref.fa"
-        #if str($reference_source.reference_source_selector) == "history":
-            ln -s '${reference_source.database}' '${reference_fasta_filename}'
-        #else:
+      #if str($reference_source.reference_source_selector) == "history":
+            #set $reference_fasta_filename = "localref.fa" 
+            ln -s '${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
-        '${reference_fasta_filename}'
-        '${query}'
-        output
-    && sort -k 10,10 -k 12,12n output > '${output_sorted}'
+      #end if
+      blat 
+            #if $noHead == "yes"
+            -noHead
+            #end if
+            -q=$query_type
+            -t=$database_type
+            -mask=$mask
+            '$reference_fasta_filename'
+            '${query}'
+            output
+      && sort -k 10,10 -k 12,12n output > '${output_sorted}'
 ]]></command>
       <inputs>
             <conditional name="reference_source">
@@ -32,6 +32,7 @@
                   <when value="cached">
                         <param name="database" type="select" label="Select database">
                               <options from_data_table="all_fasta">
+                                    <filter type="sort_by" column="2" />
                               </options>
                               <validator type="no_options" message="A built-in database is not available" />
                         </param>
@@ -90,6 +91,16 @@
             <param name="mask" value="lower" />
             <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
       </test>
+      <test>
+            <param name="reference_source_selector" value="cached" />
+            <param name="database" value="dbia3" />
+            <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
+            <param name="database_type" value="dnax" />    
+            <param name="query_type" value="rnax" />     
+            <param name="noHead" value="yes" />
+            <param name="mask" value="lower" />
+            <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
+      </test>
 
   </tests> 
   <help>
diff -r 275949b792a4 -r 355af6f61974 test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Fri May 12 17:22:07 2017 -0400
@@ -0,0 +1,30 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
+dbia3   dm3     Dbia3   /home/galaxy/galaxy/tool-data/dm3/seq/dbia3.fa
\ No newline at end of file