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author mvdbeek
date Sat, 22 Dec 2018 04:15:47 -0500
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1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.1.0" hidden="false" >
0
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2 <description>Analyze mismatch frequencies in BAM/SAM alignments</description>
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3 <requirements>
2
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4 <requirement type="package" version="0.8.3">pysam</requirement>
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5 <requirement type="package" version="0.19.0">pandas</requirement>
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6 <requirement type="package" version="1.5.3">matplotlib</requirement>
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7 </requirements>
2
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8 <command detect_errors="aggressive"><![CDATA[
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9 python '$__tool_directory__'/mismatch_frequencies.py --input
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10 #for i in $rep
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11 "$i.input_file"
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12 #end for
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13 --name
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14 #for i in $rep
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15 "$i.input_file.element_identifier"
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16 #end for
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17 --output_pdf '$output_pdf'
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18 --output_tab '$output_tab'
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19 --min $min_length
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20 --max $max_length
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21 --n_mm $number_of_mismatches
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22 --five_p $five_p
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23 --three_p $three_p
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24 --expanded_output_tab '$expanded_tab'
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25 --possible_mismatches $possible_mismatches
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26 ]]></command>
0
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27 <inputs>
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28 <repeat name="rep" title="alignment files">
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29 <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which to analyze the mismatches."/>
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30 </repeat>
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31 <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"/>
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32 <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">
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33 <validator type="expression" message="Allowed values are AGCTN, seperated by space.">len([False for char in value if not char in " AGCTN"]) == 0</validator>
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34 </param>
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35 <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/>
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36 <param name="max_length" label="Maximum read length to analyse" type="integer" value="21"/>
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37 <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/>
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38 <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"/>
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39 <param help="Output expanded tabular format" label="Nucleotide mismatches per reference sequence" name="expanded" type="select">
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40 <option selected="true" value="false">No</option>
0
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41 <option value="expanded">Yes</option>
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42 </param>
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43 </inputs>
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44 <outputs>
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45 <data format="tabular" name="output_tab" />
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46 <data format="tabular" name="expanded_tab">
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47 <filter> expanded == "expanded"</filter>
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48 </data>
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49 <data format="pdf" name="output_pdf" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" />
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54 <param name="rep_1|input_file" value="3mismatches_ago2ip_ovary.bam" ftype="bam" />
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55 <param name="number_of_mismatches" value="1" />
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56 <param name="min_length" value="21" />
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57 <param name="max_length" value="21" />
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58 <param name="three_p" value="0" />
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59 <param name="five_p" value="0" />
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60 <output name="tabular" file="mismatch.tab" ftype="tabular"/>
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61 <!--
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62 <output name="pdf" file="mismatch.pdf" ftype="pdf"/>
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63 -->
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64 </test>
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65 </tests>
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66 <help>
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67
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68 .. class:: infomark
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69
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70
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71 ***What it does***
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72
2
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73 This tool reconstitues for each aligned read of an alignment file in SAM/BAM
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74 format whether a mismatch is annotated in the MD tag, and if that is the case
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75 counts the identity of the mismatch relative to the reference sequence. The
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76 output is a PDF document with the calculated frequency for each mismatch that
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77 occured relative to the total number of valid reads and a table with the
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78 corresponding values. Read length can be limited to a specific read length, and
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79 5 prime and 3 prime-most nucleotides of a read can be ignored.
0
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80
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81 ----
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82
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83 .. class:: warningmark
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84
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85 ***Warning***
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86
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87 This tool skips all read that have insertions and has been tested only with bowtie and bowtie2
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88 generated alignment files.
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89
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90 Written by Marius van den Beek, m.vandenbeek at gmail . com
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91 </help>
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92 <citations>
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93 </citations>
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94 </tool>