--- a/tools/naive_variant_caller.xml	Mon Sep 16 10:41:15 2013 -0400
+++ b/tools/naive_variant_caller.xml	Tue Feb 04 17:26:26 2014 -0500
@@ -43,10 +43,14 @@
          --min_mapping_quality "${min_mapping_quality}"
      #end if
      
-     --coverage_dtype "${coverage_dtype}"
-     
      --allow_out_of_bounds_positions
      
+     #if str( $advanced_options.advanced_options_selector ) == "advanced":
+         --coverage_dtype "${advanced_options.coverage_dtype}"
+         ${advanced_options.safe}
+     #else
+         --coverage_dtype "uint64"
+     #end if 
   </command>
   <inputs>
     <conditional name="reference_source">
@@ -93,12 +97,24 @@
     
     <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
     
-    <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
-      <option value="uint8">uint8</option>
-      <option value="uint16" selected="True">uint16</option>
-      <option value="uint32">uint32</option>
-      <option value="uint64">uint64</option>
-    </param>
+    <conditional name="advanced_options">
+        <param name="advanced_options_selector" type="select" label="Show Advanced Options">
+            <option value="basic" selected="True">Hide Advanced Options</option>
+            <option value="advanced">Show Advanced Options</option>
+        </param>
+        <when value="basic">
+            <!-- Do nothing here -->
+        </when>
+        <when value="advanced">
+            <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
+                <option value="uint8">uint8</option>
+                <option value="uint16">uint16</option>
+                <option value="uint32">uint32</option>
+                <option value="uint64" selected="True">uint64</option>
+            </param>
+            <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/>
+        </when>
+    </conditional>
     
   </inputs>
   <outputs>
@@ -200,6 +216,7 @@
           <param name="ploidy" value="2" />
           <param name="variants_only" value="False" />
           <param name="use_strand" value="False" />
+          <param name="advanced_options_selector" value="advanced" />
           <param name="coverage_dtype" value="uint8" />
           <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
       </test>