--- a/gemini_annotate.xml	Wed Oct 17 13:31:50 2018 -0400
+++ b/gemini_annotate.xml	Fri Dec 14 12:44:52 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.2">
     <description>adding your own custom annotations</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -12,21 +12,21 @@
 
     ## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz
     #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext
-    bgzip -c "$annotate_source" > $tabixed_file &&
-    tabix -p "$annotate_source.ext" $tabixed_file &&
+    bgzip -c '$annotate_source' > '$tabixed_file' &&
+    tabix -p '$annotate_source.ext' '$tabixed_file' &&
+    cp '$infile' '$outfile' &&
 
-        gemini @BINARY@
-            -f $tabixed_file
-            -c $column_name
-            -a $a.a_selector
-            #if $a.a_selector == 'extract':
-                -t $a.column_type
-                -e $a.column_extracts
-                -o $a.operation
-            #end if
-            $region_only
-            "${ infile }"
-            > "${ outfile }"
+    gemini @BINARY@
+        -f '$tabixed_file'
+        -c '$column_name'
+        -a $a.a_selector
+        #if $a.a_selector == 'extract':
+            -t $a.column_type
+            -e '$a.column_extracts'
+            -o $a.operation
+        #end if
+        $region_only
+        '$outfile'
 ]]>
 
     </command>
@@ -36,7 +36,7 @@
 
         <param name="column_name" type="text" value=""
             label="The name of the column to be added to the variant table" 
-            help=" If the input file is a VCF, then this is the name of the info field to pull. (-c)">
+            help="If the input file is a VCF, then this is the name of the info field to pull. (-c)">
             <sanitizer invalid_char=" ">
                 <valid initial="string.letters,string.digits">
                     <add value="_" />
@@ -87,15 +87,15 @@
                 variant values. This option is only valid if annotation is a VCF file"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" />
+        <data name="outfile" format="gemini.sqlite" />
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="gemini_annotate_input.db" ftype="gemini.sqlite" />
+            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
             <param name="annotate_source" value="anno.bed" />
             <param name="a_selector" value="count" />
             <param name="column_name" value="anno5" />
-            <output name="outfile" file="gemini_annotate_result.tabular" />
+            <output name="outfile" file="gemini_annotate_result.db" ftype="gemini.sqlite" compare="sim_size" delta="1000"/>
         </test>
     </tests>
     <help><![CDATA[