--- a/bcftools_csq.xml	Thu Feb 21 16:03:33 2019 -0500
+++ b/bcftools_csq.xml	Wed Jun 05 13:09:13 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>Haplotype aware consequence predictor</description>
     <macros>
         <token name="@EXECUTABLE@">csq</token>
@@ -12,7 +12,7 @@
     <command detect_errors="aggressive"><![CDATA[
 @PREPARE_ENV@
 @PREPARE_INPUT_FILE@
-#set $section = $sec_required
+#set $section = $sec_required.reference_source
 @PREPARE_FASTA_REF@
 
 #set $section = $sec_restrict
@@ -22,21 +22,20 @@
 bcftools @EXECUTABLE@
 
 ## csq required inputs section
-#set $section = $sec_required
+#set $section = $sec_required.reference_source
 @FASTA_REF@
---gff-annot '$section.gff_annot'
+--gff-annot '$sec_required.gff_annot'
 
 ## csq options section
-#set $section = $sec_csq_opts
-#if str($section.ncsq):
-    --ncsq $section.ncsq
+#if str($sec_csq_opts.ncsq):
+    --ncsq $sec_csq_opts.ncsq
 #end if
-$section.local_csq
-#if $section.phase:
-    --phase $section.phase
+$sec_csq_opts.local_csq
+#if $sec_csq_opts.phase:
+    --phase $sec_csq_opts.phase
 #end if
-#if str($section.custom_tag):
-    --custom-tag '$section.custom_tag'
+#if str($sec_csq_opts.custom_tag):
+    --custom-tag '$sec_csq_opts.custom_tag'
 #end if
 
 ## Subset section
@@ -85,8 +84,8 @@
         </section>
 
         <section name="sec_restrict" expanded="false" title="Restrict to">
-            <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 +100,7 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="csq.vcf" />
-            <param name="fasta_ref" ftype="fasta" value="csq.fa" />
+            <expand macro="test_using_reference" ref="csq.fa" />
             <param name="gff_annot" ftype="gff3" value="csq.gff3" />
             <param name="output_type" value="v" />
             <output name="output_file">
@@ -110,6 +109,18 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input_file" ftype="vcf" dbkey="?" value="csq.vcf" />
+            <expand macro="test_using_reference" select_from="cached" ref="csq" />
+            <param name="gff_annot" ftype="gff3" value="csq.gff3" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="BCSQ" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 =====================================