# HG changeset patch
# User mvdbeek
# Date 1431344710 14400
# Node ID e3d950e52e383a14598aa0618270379abd70a1b8
# Parent  deac5004196792cc8b05a3bcda6a33a421e00537
Uploaded

diff -r deac50041967 -r e3d950e52e38 mismatch_frequencies.xml
--- a/mismatch_frequencies.xml	Wed Apr 01 08:35:11 2015 -0400
+++ b/mismatch_frequencies.xml	Mon May 11 07:45:10 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.6" hidden="false" >
+<tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.7" hidden="false" >
   <description>Analyze mismatch frequencies in BAM/SAM alignments</description>
   <requirements>
     <requirement type="package" version="0.7.7">pysam</requirement>
@@ -35,8 +35,41 @@
   <tests>
     <test>
       <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" />
-      <param name="rep_1|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>
+
+.. 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>
 </tool>
diff -r deac50041967 -r e3d950e52e38 test-data/mismatch.pdf
Binary file test-data/mismatch.pdf has changed
diff -r deac50041967 -r e3d950e52e38 test-data/mismatch.tab
--- a/test-data/mismatch.tab	Wed Apr 01 08:35:11 2015 -0400
+++ b/test-data/mismatch.tab	Mon May 11 07:45:10 2015 -0400
@@ -1,3 +1,3 @@
 library	readsize	A to C	A to G	A to T	C to A	C to G	C to T	G to A	G to C	G to T	T to A	T to C	T to G	total valid reads
-3mismatches_ago2ip_s2.bam	21	31	5484	69	25	40	137	156	109	188	51	196	29	43881
-3mismatches_ago2ip_ovary.bam	21	293	879	411	452	231	872	845	191	473	384	818	324	138649
+3mismatches_ago2ip_s2.bam	21	48	6503	106	68	46	173	222	144	220	90	232	40	43881
+3mismatches_ago2ip_ovary.bam	21	380	1214	524	581	278	1127	1032	239	595	483	973	394	138649