Repository revision
71:d96f6c9a39e0

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

trim sequences tool metadata
Miscellaneous
Remove the 5' and/or 3' adapters of a list of reads.
trimSequences
toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/trimSequences/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/trimSequences/1.0.0 (this tool)
trimSequences
Requirements (dependencies defined in the <requirements> tag set)
name version type
PYTHONPATH not provided set_environment
Additional information about this tool
../Java/Python/trimSequences.py -i $inputFile -f fastq
  	#if $OptionFPADP.FPADP == "Yes":
		-5 $OptionFPADP.fivePAdaptor
	#end if	  
	 #if $OptionTPADP.TPADP == "Yes":
		-3 $OptionTPADP.threePAdaptor
	#end if	
	-e $errors
	$indels
  	$noAdaptor5p $noAdaptorFile5p
  	$noAdaptor3p $noAdaptorFile3p
  	-o $outputFile  
  
  
python
False
False
Functional tests
name inputs outputs required files
Test-1 errors: 1
indels: False
OptionFPADP|fivePAdaptor: AAAA
OptionFPADP|FPADP: Yes
noAdaptor3p: False
noAdaptor5p: False
OptionTPADP|TPADP: No
inputFile: short_fastq.fastq
outputFile: exp_trimsequences_short_fastq.fastq
short_fastq.fastq
exp_trimsequences_short_fastq.fastq