# HG changeset patch
# User iuc
# Date 1475511708 14400
# Node ID cc016cb332cd6f2461a6081e0297c6badb63955f
# Parent  3e4c1bb306e9adfd430e50368545c2dd855fd2cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6

diff -r 3e4c1bb306e9 -r cc016cb332cd bcftools_view.xml
--- a/bcftools_view.xml	Wed Jul 13 11:01:08 2016 -0400
+++ b/bcftools_view.xml	Mon Oct 03 12:21:48 2016 -0400
@@ -116,9 +116,9 @@
                    help="Trim alternate alleles not seen in the subset" />
         </section>
         <section name="sec_filter" expanded="false" title="Filter Options">
-            <param name="min_ac" type="integer" label="Min Ac" default="nref" optional="True" 
+            <param name="min_ac" type="integer" label="Min Ac" optional="True" 
                    help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
-            <param name="max_ac" type="integer" label="Max Ac" default="nref" optional="True" 
+            <param name="max_ac" type="integer" label="Max Ac" optional="True" 
                    help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
             <param name="select_genotype" type="select">
                 <option value="__none__" selected="True">No selection</option>
@@ -163,9 +163,9 @@
               </param>
 
               <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
-              <param name="min_af" type="float" label="Min Af" default="nref" optional="True" 
+              <param name="min_af" type="float" label="Min Af" optional="True" 
                      help="(-q) Minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
-              <param name="max_af" type="float" label="Max Af" default="nref" optional="True" 
+              <param name="max_af" type="float" label="Max Af" optional="True" 
                      help="(-Q) Maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
 
               <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
@@ -191,7 +191,7 @@
                 <option value="--no-header">(-h) no-header</option>
                 <option value="--header-only">(-H) header-only</option>
             </param>
-            <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" default="-1" optional="True" 
+            <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True" 
                    help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
             <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File" 
                    help="Inverts the query/filtering applied by Targets File" />
diff -r 3e4c1bb306e9 -r cc016cb332cd macros.xml
--- a/macros.xml	Wed Jul 13 11:01:08 2016 -0400
+++ b/macros.xml	Mon Oct 03 12:21:48 2016 -0400
@@ -339,7 +339,6 @@
         </when>
         <when value="targets_file">
             <expand macro="macro_targets_file">
-               <optional>true</optional>
             </expand>
         </when>
     </conditional>