--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_barcode_splitter_single.xml	Tue Jul 19 13:03:32 2011 -0500
@@ -0,0 +1,63 @@
+<tool id="cshl_fastx_barcode_splitter_single" name="Barcode Splitter (Single)">
+	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
+	<command interpreter="python">fastx_barcode_splitter_single_galaxy_wrapper.py 
+           $matched_output 
+           $unmatched_output
+           "$input.ext" 
+           --barcodes='$barcode'
+           $input "$input.name"
+            --mismatches $mismatches --partial $partial $EOL 
+        </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" />
+
+    <param name="barcode" type="text" label="Barcode to extract" />
+
+    <!-- 
+                <param name="barcodes" type="select" multiple="true" label="Select barcodes to add as new datasets to history">
+		    <options from_dataset="BARCODE">
+    			<column name="name" index="0"/>
+    			<column name="value" index="0"/>
+                        <filter type="unique_value" name="unq_bc" column="0" />
+                        <filter type="add_value" name="unmatched" value="unmatched"/>
+		    </options>
+                </param>
+    -->
+	</inputs>
+
+	<outputs>
+		<data format_source="input" name="matched_output" label="Barcode Splitter on ${input.name} (Matching sequences)" />
+    <data format_source="input" name="unmatched_output" label="Barcode Splitter on ${input.name} (Unmatched sequences)" />
+	</outputs>
+	
+	<tests>
+	</tests>
+
+<help>
+
+**What it does**
+
+This tool splits a Solexa library (FASTQ file) or a regular FASTA file into two files using a barcode as the split criteria.
+
+--------
+
+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.
+
+An additional FASTQ file will be created (the 'unmatched' file), where sequences not matching this barcode will be stored.
+
+</help>
+</tool>
+<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->