## May need to symlink input if there is an associated
#set $input_vcfs = []
#set $vcfs_list_file = 'vcfs_list'
#for (i, input_file) in enumerate($input_files):
  #set $input_vcf = 'input' + str($i) + '.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') -> REQUIRES  https://github.com/galaxyproject/galaxy/pull/14605
  #elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
    ln -s '$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 $input_vcf = 'input' + str($i) + '.bcf.gz'
    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 $input_vcf &&
    #end if
  #end if
  echo '$input_vcf' >> $vcfs_list_file &&
  $input_vcfs.append($input_vcf)
#end for

  
#set $section = $sec_restrict


#set $targets_path = None
#if 'targets' in $section
  #if $section.targets.targets_src == 'targets_file':
    #set $targets_path = 'targets_file.tab.gz'
    bgzip -c "$section.targets.targets_file" > $targets_path &&
    tabix -s 1 -b 2 -e 2 $targets_path &&
  #end if
#elif $section.targets_file:
  #set $targets_path = 'targets_file.tab.gz'
  bgzip -c "$section.targets_file" > $targets_path &&
  tabix -s 1 -b 2 -e 2 $targets_path &&
#end if

  


#set $regions_path = None
#if 'regions' in $section
  #if $section.regions.regions_src == '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

  

bcftools isec

## Default section
#set $section = $sec_default
${section.complement}
#if $section.nfiles:
  --nfiles "${section.nfiles}"
#end if

#set $section = $sec_restrict


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

#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 '1') + '-' + $stop)
  #else:
    $components.append($chrom)
  #end if
#end for
#set $intervals_spec = ','.join($components)

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

  


#if $section.targets.targets_src != '__none__':
  #if $section.targets.targets_src == 'targets':
    #set $intervals = $section.targets.target_specs
    

#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 '1') + '-' + $stop)
  #else:
    $components.append($chrom)
  #end if
#end for
#set $intervals_spec = ','.join($components)

  
    --targets '${section.targets.invert_targets_file}$intervals_spec'
  #elif $section.targets.targets_src == 'targets_file':
    #if $targets_path:
      --targets-file '${section.targets.invert_targets_file}${targets_path}'
    #else:
      --targets-file '${section.targets.invert_targets_file}${section.targets.targets_file}'
    #end if
  #end if
  #if 'targets_overlap' in $section.targets:
    --targets-overlap $section.targets.targets_overlap
  #end if
#end if

  

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

#if $section.apply_filters:
  --apply-filters '${section.apply_filters}'
#end if
  

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

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


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

  --threads \${GALAXY_SLOTS:-4}
  

## Primary Input/Outputs

#echo ' '.join($input_vcfs)#
  
> '$output_file'