Mercurial > repos > mvdbeek > mismatch_frequencies
comparison mismatch_frequencies.xml @ 12:848d799e6fe8
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| author | mvdbeek |
|---|---|
| date | Tue, 31 Mar 2015 09:43:20 -0400 |
| parents | |
| children | 7c5b252bf6af |
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| 11:f69b6df76e0e | 12:848d799e6fe8 |
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| 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.5" hidden="false" > | |
| 2 <description>Analyze mismatch frequencies in BAM/SAM alignments</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.8.1">pysam</requirement> | |
| 5 <requirement type="package" version="0.14.1">pandas</requirement> | |
| 6 <requirement type="package" version="1.4">matplotlib</requirement> | |
| 7 </requirements> | |
| 8 <command interpreter="python">mismatch_frequencies.py --input | |
| 9 #for i in $rep | |
| 10 "$i.input_file" | |
| 11 #end for | |
| 12 --name | |
| 13 #for i in $rep | |
| 14 "$i.input_file.name" | |
| 15 #end for | |
| 16 --output_pdf $output_pdf --output_tab $output_tab --min $min_length --max $max_length | |
| 17 --n_mm $number_of_mismatches | |
| 18 --five_p $five_p | |
| 19 --three_p $three_p | |
| 20 </command> | |
| 21 <inputs> | |
| 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 you want to calculate mismatch frequencies."/> | |
| 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"/> | |
| 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"/> | |
| 28 <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/> | |
| 29 <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"/> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data format="tabular" name="output_tab" /> | |
| 33 <data format="pdf" name="output_pdf" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="rep_0|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" /> | |
| 40 <param name="min_length" value="21" /> | |
| 41 <param name="max_length" value="21" /> | |
| 42 <output name="tabular" file="mismatch.tab" ftype="tabular"/> | |
| 43 </test> | |
| 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> | |
| 70 </tool> |