Repository revision
71:d96f6c9a39e0

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

get introns tool metadata
Miscellaneous
get introns
Get the introns of a set of transcripts.
getIntrons
toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/getIntrons/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/getIntrons/1.0.0 (this tool)
getIntrons
Requirements (dependencies defined in the <requirements> tag set)
name version type
PYTHONPATH not provided set_environment
Additional information about this tool
../Java/Python/getIntrons.py -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName == 'gff':
			-f gff
		#elif $formatType.FormatInputFileName == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName == 'gff3':
			-f gff3
		#elif $formatType.FormatInputFileName == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf
		#end if
		-o $outputFileGff 
	
python
False
False
Functional tests
name inputs outputs required files
Test-1 formatType|inputFileName: genes.gtf
formatType|FormatInputFileName: gtf
outputFileGff: exp_getIntrons.gff3
genes.gtf
exp_getIntrons.gff3