Repository revision
71:d96f6c9a39e0

Repository 's_mart'
hg clone https://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart

get difference tool metadata
Miscellaneous
Gets all the regions of the genome, except the one given in an annotation file. Alternatively, it may also give all the elements from the first set which does not ovelap with the second set (at the nucleotide level).
getDifference
toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/getDifference/1.0.0
1.0.0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/getDifference/1.0.0 (this tool)
getDifference
Requirements (dependencies defined in the <requirements> tag set)
name version type
PYTHONPATH not provided set_environment
Additional information about this tool
../Java/Python/getDifference.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

		$split
		
		#if $OptionSequence.option == "Yes":
			-s $OptionSequence.sequence
		#end if
		
		-o $outputFileGff


	
python
False
False
Functional tests
No functional tests defined