Mercurial > repos > iuc > bcftools_mpileup

comparison bcftools_mpileup.xml @ 12:31ea13dfe5e6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 407e1d8f4dd1a60623783331926098f7f5624841
author iuc
date Fri, 19 Aug 2022 19:51:22 +0000
parents 6d7dc9a1bef3
children 37757ffb4c5f
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11:f506df85c652 12:31ea13dfe5e6
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> 3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">mpileup</token> 5 <token name="@EXECUTABLE@">mpileup</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <xml name="bam_flag_options"> 7 <xml name="bam_flag_options">
106 #if $section.filter_by_flags.exclude_flags: 106 #if $section.filter_by_flags.exclude_flags:
107 --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])} 107 --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])}
108 #end if 108 #end if
109 #end if 109 #end if
110 -d "${section.max_reads_per_bam}" 110 -d "${section.max_reads_per_bam}"
111 $section.ignore_overlaps
111 ${section.skip_anomalous_read_pairs} 112 ${section.skip_anomalous_read_pairs}
112 #if str( $section.quality.quality_settings ) == "adjust": 113 #if str( $section.quality.quality_settings ) == "adjust":
113 $section.quality.baq 114 $section.quality.baq
114 -q "${section.quality.minimum_mapping_quality}" 115 -q "${section.quality.minimum_mapping_quality}"
115 -Q "${section.quality.minimum_base_quality}" 116 -Q "${section.quality.minimum_base_quality}"