<tool id="trimming3" name="Trim 3' adapter">
  <description> using FASTX Toolkit</description>
  
  <command>
	fastx_clipper -a $adapterSeq -l $discardShorterThan $discardNonclipped $discardClipped $adapterOnly $keepUnknown   
	#if $minAdapterAlignment.minOverlapRequired =="yes":
		-M $minAdapterAlignment.minLen
	#end if	
	-v -i $input 2>/dev/null | fastq_quality_trimmer -v -l $discardShorterThan -t $qualityThreshold -o $output
  </command>

  <inputs>
	<param name="input" type="data" format="fastq" label="Input FASTQ file"/>
    
	<param name="adapterSeq" type="text" value="" label="Adapter sequence (the 3' adapter will vary for different CLIP protocol variations)"/>
        <param name="discardShorterThan" type="integer" value="" label="Discard sequences shorter than N nucleotides (see help below for parameter suggestion)"/>
	<param name="discardNonclipped" type="boolean" truevalue="-c" falsevalue="" checked="no" label="Discard non-trimmed sequences (i.e. - keep only sequences which contained the adapter)" />
        <param name="discardClipped" type="boolean" truevalue="-C" falsevalue="" checked="no" label="Discard trimmed sequences (i.e. - keep only sequences which did not contained the adapter)" />
        <param name="adapterOnly" type="boolean" truevalue="-k" falsevalue="" checked="no" label="Report Adapter-Only sequences"/>
        <param name="keepUnknown" type="boolean" truevalue="-n" falsevalue="" checked="yes"  label="Keep sequences with unknown nucleotides"/>
	<conditional name="minAdapterAlignment">
		<param name="minOverlapRequired" type="select" label="Require minimum adapter alignment length of N. If less than N nucleotides aligned with the adapter - don't trim it.">
			<option value="yes">Yes</option>
			<option value="no" selected="True">No</option>
		</param>
		<when value="yes">
			<param name="minLen" type="integer" value="" label="Input the length"/>
		</when>
		<when value="no">
		</when>
	</conditional>
        <param name="qualityThreshold" type="integer" value="5" label="Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence)"/>
        <!--<param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/> -->
 
  </inputs>
  
  <outputs>
	<data name="output" format="fastq" label="Trim 3' adapter on ${on_string} "/>
  </outputs>
  <help>

.. class:: infomark

**What this tool does**


This tool takes as input FASTQ files and output FASTQ files with 3' adapters and extremely low quality bases (e.g. score less than 5) removed. 

It is a wrapper of fastx_clipper and fastq_quality_trimmer that are a part of the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).

-----

**Parameter suggestion for discarding sequences**

We typically require high quality score in barcode and 15 nt of CLIP tags.
* For standard CLIP: discard sequences shorter than 20 nt (5 nt barcode + 15 nt CLIP tag).
* For BrdU CLIP: discard sequences shorter than 29 nucleotides (14 nt barcode + 15 nt CLIP tag).

  </help>

</tool>