comparison bcftools_mpileup.xml @ 18:bf533509c5b6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5b9441b69b3c176ab7b89609495f66cb29d1091a

17:56556e1267de

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <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">

    -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
    --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
    -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
    ${section.perform_indel_calling.gapped_read_per_sample}
    #if len( $section.perform_indel_calling.platform_list_repeat ):
        -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
    #end if
#end if

#if $section.ambig_reads
    --ambig-reads $section.ambig_reads

18:bf533509c5b6

<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
    <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">

    -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
    --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
    -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
    ${section.perform_indel_calling.gapped_read_per_sample}
    #if len( $section.perform_indel_calling.platform_list_repeat ):
        -P "${ ",".join( [ str( platform['platform_entry'] ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
    #end if
#end if

#if $section.ambig_reads
    --ambig-reads $section.ambig_reads