# HG changeset patch
# User iuc
# Date 1660938682 0
# Node ID 31ea13dfe5e6d76604e7cf7a66c189279c71da3b
# Parent  f506df85c652c0fec98b5190ca26f7f558030620
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 407e1d8f4dd1a60623783331926098f7f5624841

diff -r f506df85c652 -r 31ea13dfe5e6 bcftools_mpileup.xml
--- a/bcftools_mpileup.xml	Sat Jul 23 13:40:56 2022 +0000
+++ b/bcftools_mpileup.xml	Fri Aug 19 19:51:22 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