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

  
#set $input_vcf = None
#if $convert.convert_from == 'gvcf':
  #set $input_vcf = 'input.vcf.gz'
  #if $convert.input_file.is_of_type('vcf')
    bgzip -c '$convert.input_file' > $input_vcf &&
    bcftools index $input_vcf &&
  #elif $convert.input_file.is_of_type('vcf_bgzip')
    ln -s '$convert.input_file' $input_vcf
  #elif $convert.input_file.is_of_type('bcf')
    #set $input_vcf = 'input.bcf'
    ln -s '$convert.input_file' $input_vcf &&
    bcftools index $input_vcf &&
  #elif $convert.input_file.is_of_type('bcf_bgzip')
    ln -s '$convert.input_file' $input_vcf &&
  #end if
#end if
#if $convert.convert_from == 'gvcf' or $convert.convert_from == 'tsv':
  #set $section = $convert.reference_source
  

#set $input_fa_ref = None
#if 'fasta_ref' in $section and $section.fasta_ref:
  #if 'reference_source_selector' in $section:
    #if str($section.reference_source_selector) == "history":
      #set $input_fa_ref = 'ref.fa'
      ln -s '$section.fasta_ref' $input_fa_ref &&
      samtools faidx $input_fa_ref &&
    #else:
      #set $input_fa_ref = str($section.fasta_ref.fields.path)
    #end if
  #end if
#end if

  
#end if

bcftools convert


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

#if $convert.convert_from == 'gen_sample':
  --gensample2vcf '$convert.input_file,$convert.input_sample'
#elif $convert.convert_from == 'hap_sample':
  --hapsample2vcf '$convert.input_file,$convert.input_sample'
#elif $convert.convert_from == 'hap_legend_sample':
  --haplegendsample2vcf '$convert.input_file,$convert.input_legend,$convert.input_sample'
#elif $convert.convert_from == 'gvcf':
   
#if $input_fa_ref is not None:
  --fasta-ref $input_fa_ref
#elif 'fasta_ref' in $section and $section.fasta_ref:
  --fasta-ref '${section.fasta_ref}'
#end if
  
   --gvcf2vcf $input_vcf
#elif $convert.convert_from == 'tsv':
   
#if $input_fa_ref is not None:
  --fasta-ref $input_fa_ref
#elif 'fasta_ref' in $section and $section.fasta_ref:
  --fasta-ref '${section.fasta_ref}'
#end if
  
   #set $section = $convert
   
#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 $section.columns != '':
  --columns '${section.columns}'
#end if
  
   --tsv2vcf '$convert.input_file'
#end if
> '$output_file'