--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_reverse_complement.xml	Wed Jul 10 06:13:48 2013 -0400
@@ -0,0 +1,68 @@
+<tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
+	<description></description>
+	<command>
+cat '$input' |
+fastx_reverse_complement
+#if $input.ext == "fastqsanger":
+ -Q 33
+#elif $input.ext == "fastq":
+ -Q 64
+#end if
+ -v -o '$output'
+</command>
+	<inputs>
+		<param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
+	</inputs>
+
+	<tests>
+		<test>
+			<!-- Reverse-complement a FASTA file -->
+			<param name="input" value="fastx_rev_comp1.fasta" /> 
+			<output name="output" file="fastx_reverse_complement1.out" />
+		</test>
+		<test>
+			<!-- Reverse-complement a FASTQ file -->
+			<param name="input" value="fastx_rev_comp2.fastq" />
+			<output name="output" file="fastx_reverse_complement2.out" />
+		</test>
+	</tests>
+
+	<outputs>
+		<data format="input" name="output" metadata_source="input"
+		/>
+	</outputs>
+
+<help>
+**What it does**
+
+This tool reverse-complements each sequence in a library.
+If the library is a FASTQ, the quality-scores are also reversed.
+
+--------
+
+**Example**
+
+Input FASTQ file::
+
+    @CSHL_1_FC42AGWWWXX:8:1:3:740
+    TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
+    +CSHL_1_FC42AGWWWXX:8:1:3:740
+    33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
+
+
+Output FASTQ file::
+
+    @CSHL_1_FC42AGWWWXX:8:1:3:740
+    TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
+    +CSHL_1_FC42AGWWWXX:8:1:3:740
+    26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+ 
+</help>
+</tool>
+<!-- FASTX-reverse-complement is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->