--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RNA_fragment_size.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -0,0 +1,76 @@
+<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@">
+    <description>
+     calculates the fragment size for each gene/transcript
+    </description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command>
+
+    <command><![CDATA[
+        ln -sf '${input}' 'input.bam' &&
+        ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
+        RNA_fragment_size.py -i 'input.bam' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
+        ]]>
+    </command>
+
+    <inputs>
+        <expand macro="bam_param" />
+        <expand macro="refgene_param" />
+        <expand macro="mapq_param" />
+        <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)" />
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
+            <output name="output" file="output.RNA_fragment_size.txt" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+RNA_fragment_size.py
+++++++++++++++++++++
+
+Calculate fragment size for each gene/transcript. For each transcript, it will
+report : 1) Number of fragment that was used to estimate mean, median, std (see
+below). 2) mean of fragment size 3) median of fragment size 4) stdev of fragment
+size.
+
+Inputs
+++++++
+
+Input BAM/SAM file
+    Alignment file in BAM/SAM format.
+
+Reference gene model
+    Reference gene model in BED format. Must be strandard 12-column BED file.
+    [required]
+
+Minimum mapping quality
+    Minimum mapping quality for an alignment to be considered as "uniquely
+    mapped". default=30
+
+Minimum number of fragments
+    Minimum number of fragments. default=3
+
+@ABOUT@
+
+]]>
+
+    </help>
+
+    <expand macro="citations" />
+
+</tool>