Repository revision
71:d96f6c9a39e0

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

get differential expression tool metadata
Miscellaneous
Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file.
GetDifferentialExpression
toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/GetDifferentialExpression/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/GetDifferentialExpression/1.0.0 (this tool)
GetDifferentialExpression
Requirements (dependencies defined in the <requirements> tag set)
name version type
PYTHONPATH not provided set_environment
Additional information about this tool
../Java/Python/GetDifferentialExpression.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
			
		-k $formatTypeRef.inputFileNameRef
		#if $formatTypeRef.FormatInputFileNameRef == 'bed':
			-l bed
		#elif $formatTypeRef.FormatInputFileNameRef == 'gff':
			-l gff	
		#elif $formatTypeRef.FormatInputFileNameRef == 'gff2':
			-l gff2
		#elif $formatTypeRef.FormatInputFileNameRef == 'gff3':
			-l gff3
		#elif $formatTypeRef.FormatInputFileNameRef == 'sam':
			-l sam
		#elif $formatTypeRef.FormatInputFileNameRef == 'gtf':
			-l gtf
		#end if
		
		-o $outputFileGff 
		
		$simple
		$adjusted

		#if $optionSimplePara.simplePara == 'Yes':
			-S $optionSimplePara.paraValue
		#end if		
		
		#if $optionFixedSizeFactor.FSF == 'Yes':
			-x $optionFixedSizeFactor.FSFValue
		#end if
		
		#if $optionFDR.FDR == 'Yes':
			-d $optionFDR.FDRValue
		#end if
	
python
False
False
Functional tests
No functional tests defined