<tool id="cshl_fastq_masker" name="Mask nucleotides">
	<description>(based on quality)</description>
	<command>
		cat '$input' |
		fastq_masker
#if $input.ext == "fastqsanger":
 -Q 33
#elif $input.ext == "fastq":
 -Q 64
#end if
 -v -q $cutoff -r '$maskchar' -o '$output'</command>
	<inputs>
		<param format="fastq,fastqsanger" name="input" type="data" label="Library to clip" />

		<param name="cutoff" size="4" type="integer" value="20">
			<label>Minimum quality score</label>
			<help>Nucleotides below this quality will be masked</help>
		</param>

		<param name="maskchar" size="1" type="text" value="N">
			<label>Mask character</label>
			<help>Replace low-quality nucleotides with this character. Common values: 'N' or '.'</help>
		</param>
	</inputs>

	<tests>
		<test>
			<param name="input" value="fastq_masker.fastq" ftype="fastq" />
			<param name="cutoff" value="29"/>
			<param name="maskchar" value="x"/>
			<output name="output" file="fastq_masker.out" />
		</test>
	</tests>

	<outputs>
		<data format="input" name="output" metadata_source="input" 
		/>
	</outputs>
	<help>
**What it does**

This tool masks low-quality nucleotides in a FASTQ file, and replaces them with the specifed mask character (**N** by default).

--------

**Example**

Input FASTQ file::

    @1
    TATGGTCAGAAACCATATGC
    +1
    40 40 40 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19
    @2
    CAGCGAGGCTTTAATGCCAT
    +2
    40 40 40 40 40 40 40 40 30 20 19 20 19 19 19 19 19 19 19 19
    @3
    CAGCGAGGCTTTAATGCCAT
    +3
    40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 19 19 19

After Masking nucleotides with quality lower than 20 with the character **N**::

    @1
    TATGGTCAGAAANNNNNNNN
    +1
    40 40 40 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19
    @2
    CAGCGAGGCTNTNNNNNNNN
    +2
    40 40 40 40 40 40 40 40 30 20 19 20 19 19 19 19 19 19 19 19
    @3
    CAGCGAGGCNNNNNNNNNNN
    +3
    40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 19 19 19


------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/

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