Mercurial > repos > iuc > bcftools_view

diff bcftools_view.xml @ 2:cc97f5b05cba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
author iuc
date Sat, 21 Jan 2017 06:57:38 -0500
parents 89dff8355de4
children b8f8fdd611ee
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line diff
--- a/bcftools_view.xml	Wed Jul 13 10:55:23 2016 -0400
+++ b/bcftools_view.xml	Sat Jan 21 06:57:38 2017 -0500
@@ -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" />