# HG changeset patch
# User iuc
# Date 1660936422 0
# Node ID fe142c9eae6cd353e42fc2f04e8e18a3ce717bb2
# Parent  3b842ed1cf33789a272dea40958cbfdda5700fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 407e1d8f4dd1a60623783331926098f7f5624841

diff -r 3b842ed1cf33 -r fe142c9eae6c bcftools_mpileup.xml
--- a/bcftools_mpileup.xml	Sat Jul 23 13:05:32 2022 +0000
+++ b/bcftools_mpileup.xml	Fri Aug 19 19:13:42 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
     <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
     <macros>
         <token name="@EXECUTABLE@">mpileup</token>
@@ -108,6 +108,7 @@
     #end if
 #end if
 -d "${section.max_reads_per_bam}"
+$section.ignore_overlaps
 ${section.skip_anomalous_read_pairs}
 #if str( $section.quality.quality_settings ) == "adjust":
     $section.quality.baq