--- a/tools/cgatools17/listvariants_v17.xml	Tue Nov 10 11:18:20 2015 -0500
+++ b/tools/cgatools17/listvariants_v17.xml	Wed Nov 11 03:51:05 2015 -0500
@@ -1,75 +1,92 @@
 <tool id="cg_listvariant" name="ListVariants" version="1.7.1">
 
-	<description>Lists all variants present in CG var or masterVar file</description> 
+    <description>Lists all variants present in CG var or masterVar file</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
+            listvariants
+            --beta
 
-	<command> <!--run executable-->
-		echo \$PATH;
-		cgatools | head -1;
-		cgatools listvariants
-		--beta
-		--reference ${crr.fields.crr_path}
-		--output $output
-		#if $include_list.listing == "yes" <!--only added when yes-->
-			--variant-listing $include_list.list
-		#end if
-		$longvar
-		--variants 
-		#for $v in $file_types.varfiles <!--get each var/mastervar file-->
-				${v.input}
-		#end for
+            #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
+            #if $include_list.listing == "yes" <!--only added when yes-->
+                --variant-listing $include_list.list
+            #end if
+            $longvar
+            --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 genome (.crr file)">
-			<options from_data_table="cg_anno_files" />
-		</param>
+    </command>
 
-		<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" min="1">
-					<param name="input" type="data" format="cg_var" label="Dataset"/>			
-				</repeat>				
-			</when>			
-			<when value="mastervar">	
-				<repeat name="varfiles" title="Variant files" min="1">
-					<param name="input" type="data" format="cg_mastervar" label="Dataset"/>
-				</repeat>					
-			</when>
-		</conditional>
+    <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>
 
-		<param name="longvar" type="select" label="List long variants?">
-			<option value="" selected="true">no</option>
-			<option value="--list-long-variants">yes</option>
-		</param>
+        <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" min="1">
+                    <param name="input" type="data" format="cg_var" label="Dataset"/>
+                </repeat>
+            </when>
+            <when value="mastervar">
+                <repeat name="varfiles" title="Variant files" min="1">
+                    <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
+                </repeat>					
+            </when>
+        </conditional>
 
-		<conditional name="include_list">
-			<param name="listing" type="select" label="Include variant listing?">
-				<option value="no" selected="true">no</option>
-				<option value="yes">yes</option>
-			</param>
-			<when value="yes">
-				<param name="list" type="data" format="tabular" label="Variant listing"/>
-			</when>
-		</conditional>
-		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>		
-	</inputs>
+        <param name="longvar" type="select" label="List long variants?">
+            <option value="" selected="true">no</option>
+            <option value="--list-long-variants">yes</option>
+        </param>
+
+        <conditional name="include_list">
+            <param name="listing" type="select" label="Include variant listing?">
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="list" type="data" format="tabular" label="Variant listing"/>
+            </when>
+        </conditional>
+        <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 listvariants to list all called variants present in the var or mastervar files.
@@ -82,50 +99,50 @@
 
 **Command line reference**::
 
-		COMMAND NAME
-		  listvariants - Lists the variants present in a variant file.
+        COMMAND NAME
+          listvariants - Lists the variants present in a variant file.
 
-		DESCRIPTION
-		  Lists all called variants present in the specified variant files, in a 
-		  format suitable for processing by the testvariants command. The output is a
-		  tab-delimited file consisting of the following columns:
-			 
-		    variantId  Sequential id assigned to each variant.
-		    chromosome The chromosome of the variant.
-		    begin      0-based reference offset of the beginning of the variant.
-		    end        0-based reference offset of the end of the variant.
-		    varType    The varType as extracted from the variant file.
-		    reference  The reference sequence.
-		    alleleSeq  The variant allele sequence as extracted from the variant 
-		               file.
-		    xRef       The xRef as extrated from the variant file.
+        DESCRIPTION
+          Lists all called variants present in the specified variant files, in a 
+          format suitable for processing by the testvariants command. The output is a
+          tab-delimited file consisting of the following columns:
+             
+            variantId  Sequential id assigned to each variant.
+            chromosome The chromosome of the variant.
+            begin      0-based reference offset of the beginning of the variant.
+            end        0-based reference offset of the end of the variant.
+            varType    The varType as extracted from the variant file.
+            reference  The reference sequence.
+            alleleSeq  The variant allele sequence as extracted from the variant 
+                       file.
+            xRef       The xRef as extrated from the variant file.
 
-		OPTIONS
-		  -h [ --help ] 
-		      Print this help message.
+        OPTIONS
+          -h [ --help ] 
+              Print this help message.
 
-		  --beta 
-		      This is a beta command. To run this command, you must pass the --beta 
-		      flag.
+          --beta 
+              This is a beta command. To run this command, you must pass the --beta 
+              flag.
 
-		  --reference arg
-		      The reference crr file.
+          --reference arg
+              The reference crr file.
 
-		  --output arg (=STDOUT)
-		      The output file (may be omitted for stdout).
+          --output arg (=STDOUT)
+              The output file (may be omitted for stdout).
 
-		  --variants arg
-		      The input variant files (may be positional args).
+          --variants arg
+              The input variant files (may be positional args).
 
-		  --variant-listing arg
-		      The output of another listvariants run, to be merged in to produce the 
-		      output of this run.
+          --variant-listing arg
+              The output of another listvariants run, to be merged in to produce the 
+              output of this run.
 
-		  --list-long-variants 
-		      In addition to listing short variants, list longer variants as well 
-		      (10's of bases) by concatenating nearby calls.
+          --list-long-variants 
+              In addition to listing short variants, list longer variants as well 
+              (10's of bases) by concatenating nearby calls.
 
-		SUPPORTED FORMAT_VERSION
-		  0.3 or later
-	</help>
+        SUPPORTED FORMAT_VERSION
+          0.3 or later
+    </help>
 </tool>