# HG changeset patch
# User mvdbeek
# Date 1427891219 14400
# Node ID a86213925f148f03bce543dc98016aacd2512bdf
# Parent  7c5b252bf6af8e0a778bd3a68e26df0f49321e17
Uploaded

diff -r 7c5b252bf6af -r a86213925f14 mismatch_frequencies.xml
--- a/mismatch_frequencies.xml	Wed Apr 01 06:04:37 2015 -0400
+++ b/mismatch_frequencies.xml	Wed Apr 01 08:26:59 2015 -0400
@@ -3,7 +3,7 @@
   <requirements>
     <requirement type="package" version="0.7.7">pysam</requirement>
     <requirement type="package" version="0.14.1">pandas</requirement>
-    <requirement type="package" version="1.4">matplotlib</requirement>
+    <requirement type="package" version="1.2">matplotlib</requirement>
   </requirements>
   <command interpreter="python">mismatch_frequencies.py --input 
 		#for i in $rep
@@ -19,8 +19,8 @@
                  --three_p $three_p
   </command>
   <inputs>
-    <repeat name="rep" title="alignment files" min="1">
-      <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which you want to calculate mismatch frequencies."/>
+    <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"/>
@@ -35,36 +35,8 @@
   <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="rep_1|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" />
       <param name="number_of_mismatches" value="1" />
       <param name="min_length" value="21" />
       <param name="max_length" value="21" />
-      <output name="tabular" file="mismatch.tab" ftype="tabular"/>
-    </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 7c5b252bf6af -r a86213925f14 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Apr 01 06:04:37 2015 -0400
+++ b/tool_dependencies.xml	Wed Apr 01 08:26:59 2015 -0400
@@ -6,7 +6,7 @@
     <package name="pandas" version="0.14.1">
         <repository changeset_revision="ef98e20431a7" name="package_pandas_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="matplotlib" version="1.4">
-        <repository changeset_revision="62a48352f6a6" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="matplotlib" version="1.2">
+        <repository changeset_revision="9f3e58477115" name="package_matplotlib_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>