--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,69 @@
+<tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter">
+	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
+	<command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command>
+
+	<inputs>
+		<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
+		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
+
+		<param name="EOL" type="select" label="Barcodes found at">
+			<option value="--bol">Start of sequence (5' end)</option>
+			<option value="--eol">End of sequence (3' end)</option>
+		</param>
+
+		<param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" />
+		
+		<param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
+	
+	</inputs>
+	
+	<tests>
+		<test>
+			<!-- Split a FASTQ file -->
+			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+			<param name="EOL" value="Start of sequence (5' end)" />
+			<param name="mismatches" value="2" />
+			<param name="partial" value="0" />
+			<output name="output" file="fastx_barcode_splitter1.out" />
+		</test>
+	</tests>
+
+	<outputs>
+		<data format="html" name="output" />
+	</outputs>
+<help>
+
+**What it does**
+
+This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
+
+--------
+
+**Barcode file Format**
+
+Barcode files are simple text files.
+Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
+Example::
+
+    #This line is a comment (starts with a 'number' sign)
+    BC1	GATCT
+    BC2	ATCGT
+    BC3	GTGAT
+    BC4 TGTCT
+    
+For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
+Sequences matching the barcode will be stored in the appropriate file.
+
+One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
+
+The output of this tool is an HTML file, displaying the split counts and the file locations.
+
+**Output Example**
+
+.. image:: ./static/fastx_icons/barcode_splitter_output_example.png
+
+</help>
+</tool>
+<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->