--- a/macros.xml	Sat Mar 11 17:57:53 2017 -0500
+++ b/macros.xml	Thu Apr 13 17:44:25 2017 -0400
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@VERSION@">1.3.1</token>
+  <token name="@VERSION@">1.4.0</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:" />
@@ -10,12 +10,14 @@
   </xml>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.3.1">bcftools</requirement>
-      <!-- conda dependency -->
-      <requirement type="package" version="1.3.2">htslib</requirement>
+      <requirement type="package" version="1.4">bcftools</requirement>
+      <requirement type="package" version="1.4">htslib</requirement>
       <yield />
     </requirements>
   </xml>
+  <xml name="samtools_requirement">
+      <requirement type="package" version="1.3.1">samtools</requirement>
+  </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
   </xml>
@@ -245,7 +247,7 @@
   </xml>
   <token name="@OUTPUT_TYPE@">
 #if str($output_type) != "__none__":
-  --output-type "${output_type}"
+  --output-type '${output_type}'
 #end if
   </token>
 
@@ -279,14 +281,30 @@
         </when>
     </conditional>
   </xml>
+  <token name="@PREPARE_REGIONS_FILE@">
+<![CDATA[
+#set $regions_path = None
+#if 'regions' in $section
+  #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
+    #if $section.regions.regions_file.ext.startswith('bed'):
+      #set $regions_path = 'regions_file.bed'
+      ln -s '$section.regions.regions_file' $regions_path &&
+    #end if
+  #end if
+#end if
+]]>
+  </token>
   <token name="@REGIONS@">
 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
   --regions '$section.regions.regions'
 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
-  --regions-file '$section.regions.regions_file'
+  #if $regions_path is not None:
+    --regions-file '$regions_path'
+  #else:
+    --regions-file '$section.regions.regions_file'
+  #end if
 #end if
   </token>
-
   <xml name="macro_targets_file">
             <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
               <yield/>
@@ -356,11 +374,11 @@
 
   <xml name="macro_samples">
       <param name="samples" type="text" value="" label="Samples" optional="true"
-             help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
+             help="(-s) comma separated list of samples to annotate (or exclude)">
           <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
       </param>
       <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
-             help="inverts the query/filtering applied by Samples" />
+             help="inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
       <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
              help="(-S) file of samples to include" />
       <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"