comparison bcftools_mpileup.xml @ 2:cf06b44624c7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69

1:9c711df3258d

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
    <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">

            <option value="64">Read is the first in a pair</option>
            <option value="128">Read is the second in a pair</option>
            <option value="256">The alignment or this read is not primary</option>
            <option value="512">The read fails platform/vendor quality checks</option>
            <option value="1024">The read is a PCR or optical duplicate</option>
         </xml>
    </macros>
    <expand macro="requirements">
        <expand macro="samtools_requirement"/>
    </expand>
    <expand macro="version_command" />

    #end if
    #set $input_name = $input_base + '.' + $ext
    #silent $bam_list.append($input_name)
    ln -s '${input.input_bam}' ${input_name} &&
    #if $input.input_bam.ext == 'bam':
      ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
    #else:
      ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
    #end if
#else:
    #for $bam_count, $input_bam in enumerate( $input.input_bams ):
        #set $input_base = $re.sub('\W','_',$input_bam.display_name.replace('.bam','').replace('.cram',''))
        #set $ext = 'bam'

    #end for
#end if

#set $input_fa_ref = None
#if $reference_source.reference_source_selector == "history":
  #set $input_fa_ref = 'ref.fa'
  ln -s '${reference_source.ref_file}' $input_fa_ref &&
  samtools faidx $input_fa_ref &&
#elif $reference_source.reference_source_selector == "cached":
  #set $input_fa_ref = $reference_source.ref_file.fields.path
#end if

#set $section = $sec_restrict
@PREPARE_REGIONS_FILE@
@PREPARE_TARGETS_FILE@

#end if

## Indel Calling section
#set $section = $sec_indel
#if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling':
  --skip-indels
#elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling':
  -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
  -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
  -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
  -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
  -m "${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

## Filter section
#set $section = $sec_filtering
#if str( $section.filter_by_flags.filter_flags ) == "filter":
  #if $section.filter_by_flags.require_flags:
    --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])}
  #end if
  #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 "${section.quality.minimum_base_quality}"
  -C "${section.quality.coefficient_for_downgrading}"
#end if
#if str( $section.read_groups.read_groups_selector ) == "ignore_rg":
  --ignore-RG
#elif str( $section.read_groups.read_groups_selector ) == "paste":
  -G "${section.read_groups.rg_action}${read_groups_file}"
#elif str( $section.read_groups.read_groups_selector ) == "history"
  -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
#end if

#set $section = $sec_output_options
#if $section.output_tags:
 --annotate "$section.output_tags"
#end if
#if $section.gvcf:
 --gvcf "$section.gvcf"
#end if

## Subset section
#set $section = $sec_subset
@SAMPLES@

## Primary Input/Outputs
#echo ' '.join($bam_list)#
> '$output_file'
#if str( $sec_filtering.read_groups.read_groups_selector ) == "paste":
&& echo 'read-groups:'
&& cat ${read_groups_file}
#end if
]]>
    </command>
    <configfiles>
        <configfile name="read_groups_file">
<![CDATA[#slurp
#set pasted_data = ''
#set $section = $sec_filtering
#if str( $section.read_groups.read_groups_selector ) == "paste":
  #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
#end if
#slurp
${pasted_data}
]]>
        </configfile>

@TARGETS_HELP@

@BCFTOOLS_MANPAGE@#@EXECUTABLE@

@BCFTOOLS_WIKI@
]]>
    </help>
    <expand macro="citations" />
</tool>

2:cf06b44624c7

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

            <option value="64">Read is the first in a pair</option>
            <option value="128">Read is the second in a pair</option>
            <option value="256">The alignment or this read is not primary</option>
            <option value="512">The read fails platform/vendor quality checks</option>
            <option value="1024">The read is a PCR or optical duplicate</option>
        </xml>
    </macros>
    <expand macro="requirements">
        <expand macro="samtools_requirement"/>
    </expand>
    <expand macro="version_command" />

    #end if
    #set $input_name = $input_base + '.' + $ext
    #silent $bam_list.append($input_name)
    ln -s '${input.input_bam}' ${input_name} &&
    #if $input.input_bam.ext == 'bam':
        ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
    #else:
        ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
    #end if
#else:
    #for $bam_count, $input_bam in enumerate( $input.input_bams ):
        #set $input_base = $re.sub('\W','_',$input_bam.display_name.replace('.bam','').replace('.cram',''))
        #set $ext = 'bam'

    #end for
#end if

#set $input_fa_ref = None
#if $reference_source.reference_source_selector == "history":
    #set $input_fa_ref = 'ref.fa'
    ln -s '${reference_source.ref_file}' $input_fa_ref &&
    samtools faidx $input_fa_ref &&
#elif $reference_source.reference_source_selector == "cached":
    #set $input_fa_ref = $reference_source.ref_file.fields.path
#end if

#set $section = $sec_restrict
@PREPARE_REGIONS_FILE@
@PREPARE_TARGETS_FILE@

#end if

## Indel Calling section
#set $section = $sec_indel
#if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling':
    --skip-indels
#elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling':
    -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
    -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
    -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
    -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
    -m "${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

## Filter section
#set $section = $sec_filtering
#if str( $section.filter_by_flags.filter_flags ) == "filter":
    #if $section.filter_by_flags.require_flags:
        --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])}
    #end if
    #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 "${section.quality.minimum_base_quality}"
    -C "${section.quality.coefficient_for_downgrading}"
#end if
#if str( $section.read_groups.read_groups_selector ) == "ignore_rg":
    --ignore-RG
#elif str( $section.read_groups.read_groups_selector ) == "paste":
    -G "${section.read_groups.rg_action}${read_groups_file}"
#elif str( $section.read_groups.read_groups_selector ) == "history"
    -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
#end if

#set $section = $sec_output_options
#if $section.output_tags:
    --annotate "$section.output_tags"
#end if
#if $section.gvcf:
    --gvcf "$section.gvcf"
#end if

## Subset section
#set $section = $sec_subset
@SAMPLES@

## Primary Input/Outputs
#echo ' '.join($bam_list)#
> '$output_file'
#if str( $sec_filtering.read_groups.read_groups_selector ) == "paste":
    && echo 'read-groups:'
    && cat ${read_groups_file}
#end if
    ]]></command>
    <configfiles>
        <configfile name="read_groups_file">
<![CDATA[#slurp
#set pasted_data = ''
#set $section = $sec_filtering
#if str( $section.read_groups.read_groups_selector ) == "paste":
    #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
#end if
#slurp
${pasted_data}
]]>
        </configfile>

@TARGETS_HELP@

@BCFTOOLS_MANPAGE@#@EXECUTABLE@

@BCFTOOLS_WIKI@
    ]]></help>
    <expand macro="citations" />
</tool>