--- a/tools/cgatools17/testvariants_v17.xml	Tue Nov 10 10:13:49 2015 -0500
+++ b/tools/cgatools17/testvariants_v17.xml	Tue Nov 10 11:05:48 2015 -0500
@@ -1,61 +1,80 @@
-<tool id="cg_testvariants" name="TestVariants" version="1.7.1">
-
-	<description>Test for the presence of variants</description> 
+<tool id="cg_testvariants" name="TestVariants" version="1.7.1.b">
+    <description>Test for the presence of variants</description> 
 
-	<requirements>		
-		<requirement type="package" version="1">cgatools17</requirement>
-	</requirements>
+    <requirements>
+        <requirement type="package" version="1">cgatools17</requirement>
+    </requirements>
+
+    <version_command>cgatools | head -1</version_command>
 
-	<command> <!--run executable-->
-		cgatools | head -1;
-		cgatools testvariants
-		--beta
-		--reference ${crr.fields.crr_path}
-		--output $output
-		--input $listing
-		--variants 
-		#for $v in $file_types.varfiles <!--get each var/mastervar file-->
-			${v.input}
-		#end for
-	</command>
+    <command>
+        cgatools testvariants
+        --beta
+        --reference
+        
+            #if $reference_gene_sets_source.source_select == "indexed_filtered"
+                ${reference_gene_sets_source.crr.fields.crr_path}
+            #else if $reference_gene_sets_source.source_select == "history"
+                ${reference_gene_sets_source.crr}
+            #end if
+            
+        --output $output
+        --input $listing
+        --variants 
+        #for $v in $file_types.varfiles <!--get each var/mastervar file-->
+            ${v.input}
+        #end for
+    </command>
   
-	<inputs>
-  	<!--form field to select crr file-->
-		<param name="crr" type="select" label="Reference Build">
-			<options from_data_table="cg_anno_files" />
-		</param>
+    <inputs>
+    <!--form field to select crr file-->
+    
+        <conditional name="reference_gene_sets_source">
+            <param name="source_select" type="select" label="GFF/GTF Source">
+                <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
+                <option value="history">Use reference from the history</option>
+            </param>
+            <when value="indexed_filtered">
+                <param name="crr" type="select" label="Reference Build">
+                    <options from_data_table="cg_anno_files" />
+                </param>
+            </when>
+                <when value="history">
+                    <param name="crr" format="crr" type="data" label="Reference build" help="In crr format (you can use fasta2crr for conversion)" />
+                </when>
+        </conditional>
 
-		<!--form fields to select variant list-->
-		<param name="listing" type="data" format="tabular" label="Select variant list"/>			
+        <!--form fields to select variant list-->
+        <param name="listing" type="data" format="tabular" label="Select variant list"/>
 
-		<!--conditional to select input file type-->
-		<conditional name="file_types">
-			<param name="file_type" type="select" label="Select the input file type">
-				<option value="var" selected="true">var files</option>
-				<option value="mastervar">mastervar files</option>
-			</param>
-			<when value="var">			
-				<repeat name="varfiles" title="Variant files">
-					<param name="input" type="data" format="cg_var" label="Dataset"/>
-				</repeat>
-			</when>
-			<when value="mastervar">						
-				<repeat name="varfiles" title="Variant files">
-					<param name="input" type="data" format="cg_mastervar" label="Dataset"/>				
-				</repeat>
-			</when>
-		</conditional>
+        <!--conditional to select input file type-->
+        <conditional name="file_types">
+            <param name="file_type" type="select" label="Select the input file type">
+                <option value="var" selected="true">var files</option>
+                <option value="mastervar">mastervar files</option>
+            </param>
+            <when value="var">			
+                <repeat name="varfiles" title="Variant files">
+                    <param name="input" type="data" format="cg_var" label="Dataset"/>
+                </repeat>
+            </when>
+            <when value="mastervar">						
+                <repeat name="varfiles" title="Variant files">
+                    <param name="input" type="data" format="cg_mastervar" label="Dataset"/>				
+                </repeat>
+            </when>
+        </conditional>
 
-		<!-- prefix for output file so you dont have to manually rename history items -->
-		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>	
-	</inputs>
+        <!-- prefix for output file so you dont have to manually rename history items -->
+        <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>	
+    </inputs>
 
   
-	<outputs>
-		<data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
-	</outputs>
+    <outputs>
+        <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
+    </outputs>
 
-	<help>
+    <help>
 **What it does**
 
 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
@@ -68,43 +87,43 @@
 
 **Command line reference**::
 
-		COMMAND NAME
-		  testvariants - Tests variant files for presence of variants.
-		
-		DESCRIPTION
-		  Tests variant files for presence of variants. The output is a tab-delimited
-		  file consisting of the columns of the input variants file, plus a column 
-		  for each assembly results file that contains a character code for each 
-		  allele. The character codes have meaning as follows:
-			
-		    0 This allele of this genome is consistent with the reference at this 
-		      locus but inconsistent with the variant.
-		    1 This allele of this genome has the input variant at this locus.
-		    N This allele of this genome has no-calls but is consistent with the 
-		      input variant.
-		
-		OPTIONS
-		  -h [ --help ] 
-		      Print this help message.
-		
-		  --beta 
-		      This is a beta command. To run this command, you must pass the --beta 
-		      flag.
-		
-		  --reference arg
-		      The reference crr file.
-		
-		  --input arg (=STDIN)
-		      The input variants to test for.
-		
-		  --output arg (=STDOUT)
-		      The output file (may be omitted for stdout).
-		
-		  --variants arg
-		      The input variant files (may be passed in as arguments at the end of 
-		      the command).
-		
-		SUPPORTED FORMAT_VERSION
-		  0.3 or later
-	</help>
+        COMMAND NAME
+          testvariants - Tests variant files for presence of variants.
+        
+        DESCRIPTION
+          Tests variant files for presence of variants. The output is a tab-delimited
+          file consisting of the columns of the input variants file, plus a column 
+          for each assembly results file that contains a character code for each 
+          allele. The character codes have meaning as follows:
+            
+            0 This allele of this genome is consistent with the reference at this 
+              locus but inconsistent with the variant.
+            1 This allele of this genome has the input variant at this locus.
+            N This allele of this genome has no-calls but is consistent with the 
+              input variant.
+        
+        OPTIONS
+          -h [ --help ] 
+              Print this help message.
+        
+          --beta 
+              This is a beta command. To run this command, you must pass the --beta 
+              flag.
+        
+          --reference arg
+              The reference crr file.
+        
+          --input arg (=STDIN)
+              The input variants to test for.
+        
+          --output arg (=STDOUT)
+              The output file (may be omitted for stdout).
+        
+          --variants arg
+              The input variant files (may be passed in as arguments at the end of 
+              the command).
+        
+        SUPPORTED FORMAT_VERSION
+          0.3 or later
+    </help>
 </tool>