--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamPEFragmentSize.xml	Mon Jan 25 20:14:03 2016 -0500
@@ -0,0 +1,59 @@
+<tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
+    <description>Estimate the paired-end fragment length in a BAM file</description>
+    <macros>
+        <token name="@BINARY@">bamPEFragmentSize</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+        ln -s $bamInput one.bam &&
+        ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
+
+        @BINARY@
+            @THREADS@
+            #if $histogram:
+                --histogram ./hist.png
+            #end if
+            --plotTitle "$plotTitle"
+            one.bam
+            > $outfile
+]]>
+    </command>
+    <inputs>
+        <param name="bamInput" format="bam" type="data" label="BAM file"
+            help="The BAM file must be sorted."/>
+        <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue=""
+            label="Get the distribution of fragment lengths as a histogram"
+            help=""/>
+        <expand macro="plotTitle" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt"/>
+        <data name="histogram_outfile" from_work_dir="hist.png" format="png">
+            <filter>histogram is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
+            <param name="histogram" value="True" />
+            <param name="plotTitle" value="Test Plot" />
+            <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
+            <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+This tool samples a BAM file containing paired-end data to estimate the fragment length distribution.
+Properly paired reads are preferred for computation. The output can be obtained as a histogram.
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>