#import os

#if str($ref_source_cond.ref_source) == 'cached'
    #set ref = str($ref_source_cond.reference.fields.path)
#else:
    #set ref = $ref_source_cond.reference
#end if

## callvariants uses the file extension to determine the input format.
#set input_name = str($os.path.basename($input.file_name)) + '.bam'
ln -s '${input}' '${input_name}' &&

callvariants.sh in='${input_name}' threads=\${GALAXY_SLOTS:-4} ref='${ref}' ploidy=$ploidy
#if $output_variant_score_hist:
    shist='$output_scorehist'
#end if
#if $output_zygosity_hist:
    zhist='$output_zygosityhist'
#end if
#if $output_quality_hist:
    qhist='$output_qualityhist'
#end if
#if str($output_format) == 'vcf':
    vcf='out.vcf' && mv 'out.vcf' '$output'
#elif str($output_format) == 'gff':
    outgff='out.gff' && mv 'out.gff' '$output'
#else:
    out='output.txt' && mv 'output.txt' '$output'
#end if