<tool id="removeLowQualityBases" name="Remove low quality bases">
  <description></description>
  
  <command>
	fastq_quality_trimmer -i $input -v -l $MinimumLength $CompressOutput -t $Qualitythreshold -o $output
  </command>

  <inputs>
	<param name="input" type="data" format="fastq" label="Input FASTQ file"/>
	<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="MinimumLength"  type="integer" value="29" label="Minimum length - sequences shorter than this (after trimming) will be discarded (0 = no minimum length)"/>
        <param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/>
  </inputs>
  
  <outputs>
        <data name="output" format="fastq" />
  </outputs>
  <help>

.. class:: infomark

**What this tool does**

This tool (fastq_quality_trimmer) will remove extremely low quality bases (e.g. score less than 5). 

It will take as input FASTQ files and output FASTQ files with low quality bases removed.

It is a part of the Fastx Toolkit.

-----

**Parameter suggestion for minimum length**

* For standard CLIP: discard sequences shorter than 20 nucleotides.
* For BrdU CLIP: discard sequences shorter than 29 nucleotides.

  </help>

</tool>