--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_masker.xml	Wed Jul 10 06:13:48 2013 -0400
@@ -0,0 +1,87 @@
+<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) -->