<tool id="trimming_reads" name="TrimmingReads">
	<description>Runs TrimmingReads</description>
	<command interpreter="perl">TrimmingReads.pl -i $input -l $l_int -o out.fastq -r $r_int -q $q_int -n $len_int</command>
	<inputs>
		<param name="input" label="Input file" type="data" format="fastq"/>
		<param name="l_int" label="Left Trim Bases" type="integer" value="0" />
		<param name="r_int" label="Right Trim Bases" type="integer" value="0" />
		<param name="q_int" label="Qual Cut Off" type="integer" value="0"/>
		<param name="len_int" label="Length Cut Off" type="integer" value="0"/>
	</inputs>
	<outputs>
		<data from_work_dir="out.fastq" format="fastq" />
	</outputs>
	
	<help>
	
		Trimming Reads is a part of the NGS QC Toolkit.

		This tool trims the reads/sequences and their quality scores (in case of FASTQ file) in two ways. 
		First, it trims fixed (user-specified) number of bases from 5’ and/or 3’ end of the reads and corresponding qualities from the input FASTQ file. 
		Second, it trims low quality bases from 3’ end of the read using user-defined threshold value of quality score. 
		Input to this tool is either FASTQ or FASTA format file. 
		Options are provided to specify the number of bases to be trimmed and the quality threshold for quality based trimming.
		(http://59.163.192.90:8080/ngsqctoolkit/NGSQCToolkitv2.2.3_manual.pdf)
		
		http://59.163.192.90:8080/ngsqctoolkit/
		
		http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030619
		Patel RK, Jain M (2012). NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE, 7(2): e30619.
		
		Left Trim 
	</help>
</tool>