<tool id="cshl_fastq_quality_filter" name="Quality Filter">
	<description></description>

	<command>zcat -f '$input' | fastq_quality_filter $GZIPOUT -q $quality -p $percent -v -o $output</command>

	<inputs>
		<param format="fastqsolexa" name="input" type="data" label="Library to filter" />

		<param name="quality" size="4" type="integer" value="20">
			<label>Quality cut-off value</label>
		</param>

		<param name="percent" size="4" type="integer" value="90">
			<label>Percent of bases in sequence that must have quality equal to / higher than cut-off value</label>
		</param>

		<param name="GZIPOUT" type="select" label="Compress output file (using GZIP) ">
			<option value="-z">yes</option>
			<option value="">no</option>
		</param>
	</inputs>

	<tests>
		<test>
			<!-- Test1:  100% of bases with quality 33 or higher (pretty steep requirement...) -->
			<param name="input" value="fastq_qual_filter1.fastq" />
			<param name="quality" value="33"/>
			<param name="percent" value="100"/>
			<param name="GZIPOUT" value=""/>
			<output name="output" file="fastq_qual_filter1a.out" />
		</test>
		<test>
			<!-- Test2:  80% of bases with quality 20 or higher -->
			<param name="input" value="fastq_qual_filter1.fastq" />
			<param name="quality" value="20"/>
			<param name="percent" value="80"/>
			<param name="GZIPOUT" value=""/>
			<output name="output" file="fastq_qual_filter1b.out" />
		</test>
	</tests>

	<outputs>
		<data format="input" name="output" label="$input.tag quality-filtered" metadata_source="input" />
	</outputs>

	<help>
**What it does**

This tool filters reads based on quality scores.

.. class:: infomark

Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value.

.. class:: infomark

Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value.

--------

Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded.


**Example**::

    @CSHL_4_FC042AGOOII:1:2:214:584
    GACAATAAAC
    +CSHL_4_FC042AGOOII:1:2:214:584
    30 30 30 30 30 30 30 30 20 10

Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30).

Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30).

Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20).

	    
	</help>
</tool>
<!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->