comparison bcftools_mpileup.xml @ 12:31ea13dfe5e6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 407e1d8f4dd1a60623783331926098f7f5624841

11:f506df85c652

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
    <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
    <macros>
        <token name="@EXECUTABLE@">mpileup</token>
        <import>macros.xml</import>
        <xml name="bam_flag_options">

    #if $section.filter_by_flags.exclude_flags:
        --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])}
    #end if
#end if
-d "${section.max_reads_per_bam}"
${section.skip_anomalous_read_pairs}
#if str( $section.quality.quality_settings ) == "adjust":
    $section.quality.baq
    -q "${section.quality.minimum_mapping_quality}"
    -Q "${section.quality.minimum_base_quality}"

12:31ea13dfe5e6

<?xml version='1.0' encoding='utf-8'?>
<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>
        <import>macros.xml</import>
        <xml name="bam_flag_options">

    #if $section.filter_by_flags.exclude_flags:
        --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])}
    #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":
    $section.quality.baq
    -q "${section.quality.minimum_mapping_quality}"
    -Q "${section.quality.minimum_base_quality}"