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comparison mismatch_frequencies.xml @ 7:270681625775

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Add help text and fix for skipping the beginning/end of reads aligned in reverse orientation.
author mvdbeek
date Wed, 28 Jan 2015 13:12:56 +0100
parents a7bf987b8cc4
children
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6:a7bf987b8cc4 7:270681625775
1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.4" hidden="false" > 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.5" hidden="false" >
2 <description>Analyze mismatch frequencies in BAM/SAM alignments</description> 2 <description>Analyze mismatch frequencies in BAM/SAM alignments</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.7.7">pysam</requirement> 4 <requirement type="package" version="0.7.7">pysam</requirement>
5 <requirement type="package" version="0.14">pandas</requirement> 5 <requirement type="package" version="0.14">pandas</requirement>
6 <requirement type="package" version="1.4">matplotlib</requirement> 6 <requirement type="package" version="1.4">matplotlib</requirement>
17 --n_mm $number_of_mismatches 17 --n_mm $number_of_mismatches
18 --five_p $five_p 18 --five_p $five_p
19 --three_p $three_p 19 --three_p $three_p
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <repeat name="rep" title="alignment files"> 22 <repeat name="rep" title="alignment files" min="1">
23 <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which to analyze the mismatches."/> 23 <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."/>
24 </repeat> 24 </repeat>
25 <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"/> 25 <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"/>
26 <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/> 26 <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/>
27 <param name="max_length" label="Maximum read length to analyse" type="integer" value="21"/> 27 <param name="max_length" label="Maximum read length to analyse" type="integer" value="21"/>
28 <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/> 28 <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/>
33 <data format="pdf" name="output_pdf" /> 33 <data format="pdf" name="output_pdf" />
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37 <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" /> 37 <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" />
38 <param name="rep_1|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" /> 38 <param name="rep_1|input_file" value="3mismatches_ago2ip_ovary.bam" ftype="bam" />
39 <param name="number_of_mismatches" value="1" /> 39 <param name="number_of_mismatches" value="1" />
40 <param name="min_length" value="21" /> 40 <param name="min_length" value="21" />
41 <param name="max_length" value="21" /> 41 <param name="max_length" value="21" />
42 <output name="tabular" file="mismatch.tab" ftype="tabular"/> 42 <output name="tabular" file="mismatch.tab" ftype="tabular"/>
43 <output name="pdf" file="mismatch.pdf" ftype="pdf"/>
44 </test> 43 </test>
45 </tests> 44 </tests>
45 <help>
46
47 .. class:: infomark
48
49
50 ***What it does***
51
52 This tool reconstitues for each aligned read of an alignment file in SAM/BAM format whether
53 a mismatch is annotated in the MD tag, and if that is the case counts the identity of the
54 mismatch relative to the reference sequence. The output is a PDF document with the calculated
55 frequency for each mismatch that occured relative to the total number of valid reads and a table
56 with the corresponding values. Read length can be limited to a specific read length, and 5 prime and
57 3 prime-most nucleotides of a read can be ignored.
58
59 ----
60
61 .. class:: warningmark
62
63 ***Warning***
64
65 This tool skips all read that have insertions and has been tested only with bowtie and bowtie2
66 generated alignment files.
67
68 Written by Marius van den Beek, m.vandenbeek at gmail . com
69 </help>
46 </tool> 70 </tool>