diff blat.xml @ 19:355af6f61974 draft

planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty

--- 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>