--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq/fastq_paired_unpaired.xml	Tue Jun 07 17:21:17 2011 -0400
@@ -0,0 +1,80 @@
+<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.4">
+	<description>using the read name suffices</description>
+	<command interpreter="python">
+fastq_paired_unpaired.py $input_fastq.extension $input_fastq
+#if $output_choice_cond.output_choice=="separate"
+ $output_forward $output_reverse
+#elif $output_choice_cond.output_choice=="interleaved"
+ $output_paired
+#end if
+$output_singles
+	</command>
+	<inputs>
+		<param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
+		<conditional name="output_choice_cond">
+			<param name="output_choice" type="select" label="How to output paired reads?">
+				<option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
+				<option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option>
+			</param>
+			<!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
+			<when value="separate" />
+			<when value="interleaved" />
+		</conditional>
+	</inputs>
+	<outputs>
+		<data name="output_singles" format="input" label="Orphan or single reads"/>
+		<data name="output_forward" format="input" label="Forward paired reads">
+			<filter>output_choice_cond["output_choice"] == "separate"</filter>
+		</data>
+		<data name="output_reverse" format="input" label="Reverse paired reads">
+			<filter>output_choice_cond["output_choice"] == "separate"</filter>
+		</data>
+		<data name="output_paired" format="input" label="Interleaved paired reads">
+			<filter>output_choice_cond["output_choice"] == "interleaved"</filter>
+		</data>
+	</outputs>
+	<tests>
+	</tests>
+	<requirements>
+		<requirement type="python-module">Bio</requirement>
+	</requirements>
+	<help>
+
+**What it does**
+
+Using the common read name suffix conventions, it divides a FASTQ file into
+paired reads, and orphan or single reads.
+
+The input file should be a valid FASTQ file which has been sorted so that
+any partner forward+reverse reads are consecutive. The output files all
+preserve this sort order. Pairing are recognised based on standard name
+suffices. See below or run the tool with no arguments for more details.
+
+Any reads where the forward/reverse naming suffix used is not recognised
+are treated as orphan reads. The tool supports the /1 and /2 convention
+used by Illumina, the .f and .r convention, and the Sanger convention
+(see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details).
+
+Note that this does support multiple forward and reverse reads per template
+(which is quite common with Sanger sequencing), e.g. this which is sorted
+alphabetically:
+
+WTSI_1055_4p17.p1kapIBF
+WTSI_1055_4p17.p1kpIBF
+WTSI_1055_4p17.q1kapIBR
+WTSI_1055_4p17.q1kpIBR
+
+or this where the reads already come in pairs:
+
+WTSI_1055_4p17.p1kapIBF
+WTSI_1055_4p17.q1kapIBR
+WTSI_1055_4p17.p1kpIBF
+WTSI_1055_4p17.q1kpIBR
+
+both become:
+
+WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
+WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR
+
+	</help>
+</tool>