--- a/mismatch_frequencies.xml	Mon May 11 07:45:10 2015 -0400
+++ b/mismatch_frequencies.xml	Sun May 24 11:12:24 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.7" hidden="false" >
+<tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.8" hidden="false" >
   <description>Analyze mismatch frequencies in BAM/SAM alignments</description>
   <requirements>
     <requirement type="package" version="0.7.7">pysam</requirement>
@@ -17,19 +17,31 @@
                  --n_mm $number_of_mismatches
                  --five_p $five_p
                  --three_p $three_p
+                 --expanded_output_tab $expanded_tab
+                 --possible_mismatches $possible_mismatches
   </command>
   <inputs>
     <repeat name="rep" title="alignment files">
       <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which to analyze the mismatches."/>
     </repeat>
     <param name="number_of_mismatches" label="Maximum number of allowed mismatches per read" help="Discard reads with more than the chosen number of mismatches from the frequency calculation" type="integer" value="3"/>
+    <param name="possible_mismatches" label="Specify mismatches that should be counted" help="Ignores mismatches that are not listed" type="text" value="AC AG AT CA CG CT GA GC GT TA TC TG">
+      <validator type="expression" message="Allowed values are AGCTN, seperated by space.">len([False for char in value if not char in " AGCTN"]) == 0</validator>
+    </param>
     <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/>
     <param name="max_length" label="Maximum read length to analyse" type="integer" value="21"/>
     <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/>
     <param name="three_p" label="Ignore mismatches in the last N nucleotides of a read" help="useful to discriminate between tailing events and editing events" type="integer" value="3"/>
+    <param help="Output expanded tabular format" label="Nucleotide mismatches per reference sequence" name="expanded" type="select">
+        <option select="true" value="false">No</option>
+        <option value="expanded">Yes</option>
+    </param>
   </inputs>
   <outputs>
     <data format="tabular" name="output_tab" />
+    <data format="fasta" name="expanded_tab">
+        <filter> expanded == "expanded"</filter>
+    </data>
     <data format="pdf" name="output_pdf" />
   </outputs>
   <tests>
@@ -72,4 +84,6 @@
 
 Written by Marius van den Beek, m.vandenbeek at gmail . com
   </help>
+  <citations>
+  </citations>
 </tool>