--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_paired_reads.xml	Tue Apr 30 13:12:35 2013 -0400
@@ -0,0 +1,38 @@
+<tool id="merged_paired_reads_wrapper" version="1.0" name="Merge paired reads">
+  <requirements>
+    <requirement type='package' version="1.7">sortmerna</requirement>
+  </requirements>
+  <description>Merges two fastq paired-reads files into one file.</description>
+  <command>
+merge-paired-reads.sh $input_reads1 $input_reads2 output_file.txt
+  </command>
+  <inputs>
+    <param format="fastq" name="input_reads1" type="data"
+	   label="First reads file (fastq)" help=""/>
+    <param format="fastq" name="input_reads2" type="data"
+	   label="Second reads file (fastq)" help=""/>
+  </inputs>
+  <outputs>
+    <data format="fastq" name="output" from_work_dir="output_file.txt"
+	  label="Merged reads from ${on_string} (fastq)">
+    </data>
+  </outputs>
+  <stdio>
+    <exit_code range="2" level="fatal"
+	       description="Too few or two many arguments provided" />
+  </stdio>
+  <tests>
+    <test>
+      <param name="input_reads1" value="sortmerna_wrapper_accept1.fastq" />
+      <param name="input_reads2" value="sortmerna_wrapper_other1.fastq" />
+      <output name="output" file="merged-paired-reads_output.fastq" />
+    </test>
+  </tests>
+  <help>
+Merges two fastq paired-reads files into one file.
+
+To run merge-paired-reads::
+
+    bash merge-paired-reads.sh file1.fastq file2.fastq outputfile.fastq
+  </help>
+</tool>
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