Mercurial > repos > iuc > bcftools_annotate

diff bcftools_annotate.xml @ 5:eb782a60fc53 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author: iuc
date: Thu, 13 Apr 2017 17:44:38 -0400
parents: 7b10a015526e
children: 6a88248893c4
--- a/bcftools_annotate.xml	Sat Mar 11 17:57:17 2017 -0500
+++ b/bcftools_annotate.xml	Thu Apr 13 17:44:38 2017 -0400
@@ -34,8 +34,10 @@
     grep '^\#\#INFO' ${hdr_file} > $annotation_hdr &&
   #end if
 #end if
+#set $section = $sec_restrict
 
 bcftools @EXECUTABLE@
+@PREPARE_REGIONS_FILE@
 
 #set $section = $sec_annofile
 @COLUMNS@
@@ -65,6 +67,7 @@
 #set $section = $sec_restrict
 @INCLUDE@
 @EXCLUDE@
+@COLLAPSE@
 @REGIONS@
 @SAMPLES@
 
@@ -73,7 +76,7 @@
 
 ## Primary Input/Outputs
 @INPUT_FILE@
-> "$output_file"
+> '$output_file'
 ]]>
     </command>
     <configfiles>
@@ -143,6 +146,7 @@
         <section name="sec_restrict" expanded="false" title="Restrict to">
             <expand macro="macro_include" />
             <expand macro="macro_exclude" />
+            <expand macro="macro_collapse" />
             <expand macro="macro_regions" />
             <expand macro="macro_samples" />
         </section>