--- a/bcftools_stats.xml	Thu Feb 21 15:56:16 2019 -0500
+++ b/bcftools_stats.xml	Wed Jun 05 13:00:32 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
     <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
     <macros>
         <token name="@EXECUTABLE@">stats</token>
@@ -7,7 +7,7 @@
     </macros>
     <expand macro="requirements">
         <expand macro="samtools_requirement"/>
-        <requirement type="package" version="3.0.2">matplotlib</requirement>
+        <expand macro="matplotlib_requirement" />
         <requirement type="package" version="0.1.11">tectonic</requirement>
     </expand>
     <expand macro="version_command" />
@@ -22,15 +22,17 @@
 @PREPARE_TARGETS_FILE@
 @PREPARE_REGIONS_FILE@
 ## Stats section
+#set $section = $sec_default.reference_source
+@PREPARE_FASTA_REF@
 #set $section = $sec_default
-@PREPARE_FASTA_REF@
 @PREPARE_EXONS_FILE@
 
 bcftools @EXECUTABLE@
 
 ## Stats section
+#set $section = $sec_default.reference_source
+@FASTA_REF@
 #set $section = $sec_default
-@FASTA_REF@
 @EXONS_FILE@
 ${section.first_allele_only}
 #if $section.depth.set_depth == 'yes':
@@ -81,8 +83,8 @@
             <expand macro="macro_samples" />
             <expand macro="macro_apply_filters" />
             <expand macro="macro_collapse" />
-            <expand macro="macro_regions" />
-            <expand macro="macro_targets" />
+            <expand macro="macro_restrict" />
+            <expand macro="macro_restrict" type="target" label_type="Target" />
             <expand macro="macro_include" />
             <expand macro="macro_exclude" />
         </section>
@@ -101,7 +103,25 @@
                     <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
                 </when>
             </conditional>
-            <expand macro="macro_fasta_ref" />
+            <conditional name="reference_source">
+                <param name="reference_source_selector" type="select" label="Choose a reference genome">
+                    <option value="">Run without a reference genome</option>
+                    <option value="cached">Use a built-in genome</option>
+                    <option value="history">Use a genome from the history</option>
+                </param>
+                <when value="" />
+                <when value="cached">
+                    <param name="fasta_ref" type="select" label="Reference genome">
+                        <options from_data_table="fasta_indexes">
+                            <filter type="data_meta" column="1" key="dbkey" ref="input_file" />
+                            <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
+                        </options>
+                    </param>
+                </when>
+                <when value="history">
+                    <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
+                </when>
+            </conditional>
             <expand macro="macro_exons_file" />
             <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 
                    help="Collect stats for sites with ID separately (known vs novel)" />
@@ -154,6 +174,19 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="mpileup.vcf" />
+            <section name="sec_default">
+                <expand macro="test_using_reference" select_from="cached" ref="mpileup" />
+            </section>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
+                    <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
+                    <has_text_matching expression="ST\t0\tA>C\t16"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
             <param name="plot_title" value="Plot for mpileup.vcf" />
             <output name="output_file">
                 <assert_contents>