Repository revision

Revision: 71:d96f6c9a39e0

Repository 's_mart'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart

trim sequences tool metadata

Miscellaneous

Name: trim sequences

Description: Remove the 5' and/or 3' adapters of a list of reads.

Id: trimSequences

Guid: toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/trimSequences/1.0.0

Version: 1.0.0

Version command string: None

Display in tool panel: 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)

Requirements:

name

version

type

PYTHONPATH

not provided

set_environment

Additional information about this tool

Command:

../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

Interpreter: python

Forces a history refresh: 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