export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;

  


## May need to symlink input if there is an associated
#set $input_vcf = 'input.vcf.gz'
#if $input_file.is_of_type('vcf')
  bgzip -c '$input_file' > $input_vcf &&
  bcftools index $input_vcf &&
##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
#elif $input_file.is_of_type('vcf_bgzip')
  ln -s '$input_file' $input_vcf &&
  #if $input_file.metadata.tabix_index:
    ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
  #else
    bcftools index $input_vcf &&
  #end if
#elif $input_file.is_of_type('bcf')
  #set $input_vcf = 'input.bcf'
  ln -s '$input_file' $input_vcf &&
  #if $input_file.metadata.bcf_index:
    ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
  #else
    bcftools index $input_vcf &&
  #end if
#end if

  
#set $annotation_file = None
#set $annotation_hdr = None
#set $section = $sec_annofile
#if $section.annofile.anno_fmt == 'vcf':
  #if $section.annofile.annotations.is_of_type('vcf')
    #set $annotation_file = 'annotations.vcf.gz'
    bgzip -c '$section.annofile.annotations' > $annotation_file &&
    bcftools index $annotation_file &&
  #elif $section.annofile.annotations.is_of_type('bcf')
    #set $annotation_file = 'annotations.bcf'
    ln -s '$section.annofile.annotations' $annotation_file &&
    #if $section.annofile.annotations.metadata.bcf_index:
      ln -s '${section.annofile.annotations.metadata.bcf_index}' ${annotation_file}.csi &&
    #else
      bcftools index $annotation_file &&
    #end if
  #end if
#elif $section.annofile.anno_fmt == 'tab':
  #if $section.annofile.annotations.is_of_type('bed')
    #set $annotation_file = 'annotations.bed.gz'
    bgzip -c '$section.annofile.annotations' > $annotation_file &&
    tabix -s 1 -b 2 -e 3 $annotation_file &&
  #else:
    #set $annotation_file = 'annotations.tab.gz'
    bgzip -c '$section.annofile.annotations' > $annotation_file &&
    tabix -s 1 -b 2 -e 2 $annotation_file &&
  #end if
  #if $section.annofile.header_file:
    #set $annotation_hdr = $section.annofile.header_file
  #elif $section.annofile.header_lines:
    #set $annotation_hdr = 'annotation.hdr'
    grep '^\#\#INFO' '${hdr_file}' > $annotation_hdr &&
  #end if
#end if
#set $section = $sec_restrict

bcftools annotate


#set $regions_path = None
#if 'regions' in $section
  #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
    #if $section.regions.regions_file.ext.startswith('bed'):
      #set $regions_path = 'regions_file.bed'
      ln -s '$section.regions.regions_file' $regions_path &&
    #end if
  #end if
#end if

  

#set $section = $sec_annofile

#if $section.columns != '':
  --columns '${section.columns}'
#end if
  
#if $annotation_file:
  --annotations '${annotation_file}'
#end if
#if $annotation_hdr:
    --header-lines '${annotation_hdr}'
#end if

#if $section.set_id:
  --set-id '${section.set_id}'
#end if
#if $section.mark_sites:
  --mark-sites '${section.mark_sites}'
#end if
#if $section.min_overlap
    --min-overlap '$section.min_overlap'
#end if

#set $section = $sec_annotate
#if $section.rename_chrs:
  --rename-chrs '${section.rename_chrs}'
#end if
#if $section.remove:
  --remove '${section.remove}'
#end if
#if $section.rename_annots
    --rename-annots '$section.rename_annots'
#end if


## Default section
#set $section = $sec_restrict

#if $section.include:
  --include '${section.include}'
#end if
  

#if $section.exclude:
  --exclude '${section.exclude}'
#end if
  

#if $section.collapse:
  --collapse ${section.collapse}
#end if
  


#if $section.regions.regions_src == 'regions':
  #set $intervals = $section.regions.regions
  

#set $components = []
#for $i in $intervals:
  #set $chrom = str($i.chrom).strip()
  #set $start = str($i.start).strip()
  #set $stop = str($i.stop).strip()
  #if $start or $stop:
    $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
  #else:
    $components.append($chrom)
  #end if
#end for
#set $intervals_spec = ','.join($components)

  
  --regions '$intervals_spec'
#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
  #if $regions_path is not None:
    --regions-file '$regions_path'
  #else:
    --regions-file '$section.regions.regions_file'
  #end if
#end if
#if $section.regions_overlap
  --regions-overlap $section.regions_overlap
#end if


  

#set $samples_defined = False
#if str($section.samples) != '':
  #set $samples_defined = True
  --samples '${section.invert_samples}${section.samples}'
#end if
#if $section.samples_file:
  #set $samples_defined = True
  --samples-file "${section.invert_samples_file}${section.samples_file}"
#end if
  


#if str($output_type) != "__none__":
  --output-type '${output_type}'
#end if
  

  --threads \${GALAXY_SLOTS:-4}
  

## Primary Input/Outputs

$input_vcf
  
> '$output_file'