# HG changeset patch
# User mvdbeek
# Date 1422356170 18000
# Node ID 1609cb745999e35f3660ba6d0ed882b6a3635f6e
# Parent  e8ebe5132737d76a94ec92eda7d1fc1059bffb88
Uploaded

diff -r e8ebe5132737 -r 1609cb745999 mismatch_frequencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mismatch_frequencies.xml	Tue Jan 27 05:56:10 2015 -0500
@@ -0,0 +1,36 @@
+<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
+		--name 
+		#for i in $rep
+			"$i.input_file.name"
+		#end for
+		 --output_pdf $output_pdf --output_tab $output_tab --min $min_length --max $max_length
+                 --n_mm $number_of_mismatches
+                 --five_p $five_p
+                 --three_p $three_p
+        </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>
+
+</tool>