--- a/gemini_query.xml	Tue Feb 16 05:52:47 2016 -0500
+++ b/gemini_query.xml	Fri Dec 07 12:32:48 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
     <description>Querying the GEMINI database</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -9,17 +9,19 @@
     <expand macro="version_command" />
     <command>
 <![CDATA[
+        @PROVIDE_ANNO_DATA@
+
         gemini @BINARY@
 
             --in "${in}"
 
-            #if $gt_filter.strip():
-                --gt-filter "${gt_filter}"
-            #end if
+            #set $multiline_sql_expr = $gt_filter
+            #set $cmdln_param = "--gt-filter"
+            @MULTILN_SQL_EXPR_TO_CMDLN@
 
-            #if $sample_filter.strip():
-                --sample-filter "${sample_filter}"
-            #end if
+            #set $multiline_sql_expr = $sample_filter
+            #set $cmdln_param = "--sample-filter"
+            @MULTILN_SQL_EXPR_TO_CMDLN@
 
             $show_samples
             $show_families
@@ -35,9 +37,9 @@
             ##--format FORMAT       Format of output (JSON, TPED or default) # we will take default for the time being
             ##   --sample-delim STRING The delimiter to be used with the --show-samples option.
 
-            #if $q.strip():
-                -q "${q}"
-            #end if
+            #set $multiline_sql_expr = $q
+            #set $cmdln_param = "-q"
+            @MULTILN_SQL_EXPR_TO_CMDLN@
 
             "${ infile }"
             > "${ outfile }"