--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mismatch_profile.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -0,0 +1,89 @@
+<tool id="rseqc_mismatch_profile" name="Mismatch Profile" version="@WRAPPER_VERSION@">
+    <description>
+     calculates the distribution of mismatches across reads
+    </description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[mismatch_profile.py --version]]></version_command>
+
+    <command><![CDATA[
+        mismatch_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq}
+        ]]>
+    </command>
+
+    <inputs>
+        <expand macro="bam_param" />
+        <expand macro="readlength_param" />
+        <expand macro="readnum_param" />
+        <expand macro="mapq_param" />
+        <expand macro="rscript_output_param" />
+    </inputs>
+
+    <outputs>
+        <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf" />
+        <expand macro="xls_output_data" filename="output.mismatch_profile.xls" />
+        <expand macro="rscript_output_data" filename="output.mismatch_profile.r" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="readlength" value="101" />
+            <param name="rscript_output" value="true" />
+            <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" />
+            <output name="outputxls" file="output.mismatch_profile.xls"/>
+            <output name="outputr" file="output.mismatch_profile.r"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+mismatch_profile.py
++++++++++++++++++++
+
+Calculate the distribution of mismatches across reads.
+
+Note that the “MD” tag must exist in BAM file.
+
+Inputs
+++++++
+
+Input BAM/SAM file
+    Alignment file in BAM/SAM format.
+
+Alignment length of read
+    It is usually set to the orignial read length. For example, all these cigar
+    strings ("101M", "68M140N33M", "53M1D48M") suggest the read alignment
+    length is 101. [required]
+
+Number of aligned reads used
+    Number of aligned reads with deletions used to calculate the deletion
+    profile. default=1000000
+
+Minimum mapping quality
+    Minimum mapping quality for an alignment to be considered as "uniquely
+    mapped". default=30
+
+Sample Output
+++++++++++++++
+
+.. image:: $PATH_TO_IMAGES/mismatch_profile.png
+   :height: 600 px
+   :width: 600 px
+   :scale: 80 %
+
+@ABOUT@
+
+]]>
+
+    </help>
+
+    <expand macro="citations" />
+
+</tool>