Get the flanking regions of a set of reference.
../Java/Python/GetFlanking.py -i $formatType.inputFileName1
#if $formatType.FormatInputFileName1 == 'bed':
-f bed
#elif $formatType.FormatInputFileName1 == 'gff':
-f gff
#elif $formatType.FormatInputFileName1 == 'gff2':
-f gff2
#elif $formatType.FormatInputFileName1 == 'gff3':
-f gff3
#elif $formatType.FormatInputFileName1 == 'sam':
-f sam
#elif $formatType.FormatInputFileName1 == 'gtf':
-f gtf
#end if
-j $formatType2.inputFileName2
#if $formatType2.FormatInputFileName2 == 'bed':
-g bed
#elif $formatType2.FormatInputFileName2 == 'gff':
-g gff
#elif $formatType2.FormatInputFileName2 == 'gff2':
-g gff2
#elif $formatType2.FormatInputFileName2 == 'gff3':
-g gff3
#elif $formatType2.FormatInputFileName2 == 'sam':
-g sam
#elif $formatType2.FormatInputFileName2 == 'gtf':
-g gtf
#end if
#if $OptionUpDownStream.OptionUD == 'UpStream':
-5
#elif $OptionUpDownStream.OptionUD == 'DownStream':
-3
#end if
#if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
-c
#elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
-a
#end if
#if $OptionMax.maximum == "Yes":
-D $OptionMax.max
#end if
#if $OptionMin.minimum == "Yes":
-d $OptionMin.min
#end if
-o $outputFile