--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_paired_reads.xml	Wed Sep 25 11:29:58 2013 -0400
@@ -0,0 +1,57 @@
+<tool id="split_paired_reads" name="Split paired end reads" version="1.0.0">
+  <description></description>
+  <command interpreter="python">
+    split_paired_reads.py $input $output1 $output2
+  </command>
+    <inputs>
+        <param name="input" type="data" format="fastqsanger" label="Your paired-end file" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="fastqsanger"/>
+        <data name="output2" format="fastqsanger"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="3.fastqsanger" ftype="fastqsanger"/>
+            <output name="output1" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger"/>
+            <output name="output2" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger"/>
+        </test>
+    </tests>
+<help>
+        
+**What it does**
+ 
+Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length.  
+
+-----
+
+**Input formats**
+
+A multiple-fastq file, for example::
+
+    @HWI-EAS91_1_30788AAXX:7:21:1542:1758
+    GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+    +HWI-EAS91_1_30788AAXX:7:21:1542:1758
+    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
+
+
+-----
+
+**Outputs**
+
+One end::
+
+    @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
+    GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
+    +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
+    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
+
+The other end::
+
+    @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
+    GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+    +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
+    hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
+    
+</help>
+</tool>