--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamToFastq.xml	Tue Oct 13 17:20:34 2015 -0400
@@ -0,0 +1,39 @@
+<tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools bamtofastq
+        $tags
+        -i '$input'
+        -fq '$output'
+        #if $fq2:
+           -fq2 '$output2'
+        #end if
+    </command>
+    <inputs>
+        <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
+        <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
+        <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="FASTQ for second end.
+            Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
+    </inputs>
+    <outputs>
+        <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
+        <data format="fastq2" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
+            <filter>fq2 is True</filter>
+        </data>
+    </outputs>
+<help>
+
+**What it does**
+
+bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
+
+@REFERENCES@
+
+    </help>
+    <expand macro="citations" />
+</tool>