--- a/mismatch_frequencies.xml	Sun May 24 17:26:57 2015 +0200
+++ b/mismatch_frequencies.xml	Sun May 24 17:29:41 2015 +0200
@@ -1,11 +1,11 @@
-<tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.9" hidden="false" >
-  <description>Analyze mismatch frequencies in BAM/SAM alignments</description>
-  <requirements>
-    <requirement type="package" version="0.7.7">pysam</requirement>
-    <requirement type="package" version="0.14.1">pandas</requirement>
-    <requirement type="package" version="1.2.1">matplotlib</requirement>
-  </requirements>
-  <command interpreter="python">mismatch_frequencies.py --input 
+<tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.3" hidden="false" >
+	<description>Analyze mismatch frequencies in BAM/SAM alignments</description>
+        <requirements>
+    	    <requirement type="package" version="0.7.7">pysam</requirement>
+    	    <requirement type="package" version="0.14">pandas</requirement>
+    	    <requirement type="package" version="1.4">matplotlib</requirement>
+        </requirements>
+	<command interpreter="python">mismatch_frequencies.py --input 
 		#for i in $rep
 			"$i.input_file" 
 		#end for
@@ -17,73 +17,20 @@
                  --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>
-    <test>
-      <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" />
-      <param name="rep_1|input_file" value="3mismatches_ago2ip_ovary.bam" ftype="bam" />
-      <param name="number_of_mismatches" value="1" />
-      <param name="min_length" value="21" />
-      <param name="max_length" value="21" />
-      <param name="three_p" value="0" />
-      <param name="five_p" value="0" />
-      <output name="tabular" file="mismatch.tab" ftype="tabular"/>
-    <!--
-      <output name="pdf" file="mismatch.pdf" ftype="pdf"/>
-    -->
-    </test>
-  </tests>
-  <help>
+        </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="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"/>
+	</inputs>
+        <outputs>
+                <data format="pdf" name="output_pdf" />
+                <data format="tabular" name="output_tab" />
+        </outputs>
 
-.. class:: infomark
-
-
-***What it does***
-
-This tool reconstitues for each aligned read of an alignment file in SAM/BAM format whether
-a mismatch is annotated in the MD tag, and if that is the case counts the identity of the 
-mismatch relative to the reference sequence. The output is a PDF document with the calculated
-frequency for each mismatch that occured relative to the total number of valid reads and a table
-with the corresponding values. Read length can be limited to a specific read length, and 5 prime and 
-3 prime-most nucleotides of a read can be ignored.
-
-----
-
-.. class:: warningmark
-
-***Warning***
-
-This tool skips all read that have insertions and has been tested only with bowtie and bowtie2
-generated alignment files.
-
-Written by Marius van den Beek, m.vandenbeek at gmail . com
-  </help>
-  <citations>
-  </citations>
 </tool>