Mercurial > repos > mvdbeek > mismatch_frequencies
comparison mismatch_frequencies.xml @ 18:e3d950e52e38
Uploaded
| author | mvdbeek |
|---|---|
| date | Mon, 11 May 2015 07:45:10 -0400 |
| parents | deac50041967 |
| children | f7da7f3e2c98 |
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| 17:deac50041967 | 18:e3d950e52e38 |
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| 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.6" hidden="false" > | 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.7" 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="0.14.1">pandas</requirement> | 5 <requirement type="package" version="0.14.1">pandas</requirement> |
| 6 <requirement type="package" version="1.2.1">matplotlib</requirement> | 6 <requirement type="package" version="1.2.1">matplotlib</requirement> |
| 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 <param name="three_p" value="0" /> | |
| 43 <param name="five_p" value="0" /> | |
| 44 <output name="tabular" file="mismatch.tab" ftype="tabular"/> | |
| 45 <!-- | |
| 46 <output name="pdf" file="mismatch.pdf" ftype="pdf"/> | |
| 47 --> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help> | |
| 51 | |
| 52 .. class:: infomark | |
| 53 | |
| 54 | |
| 55 ***What it does*** | |
| 56 | |
| 57 This tool reconstitues for each aligned read of an alignment file in SAM/BAM format whether | |
| 58 a mismatch is annotated in the MD tag, and if that is the case counts the identity of the | |
| 59 mismatch relative to the reference sequence. The output is a PDF document with the calculated | |
| 60 frequency for each mismatch that occured relative to the total number of valid reads and a table | |
| 61 with the corresponding values. Read length can be limited to a specific read length, and 5 prime and | |
| 62 3 prime-most nucleotides of a read can be ignored. | |
| 63 | |
| 64 ---- | |
| 65 | |
| 66 .. class:: warningmark | |
| 67 | |
| 68 ***Warning*** | |
| 69 | |
| 70 This tool skips all read that have insertions and has been tested only with bowtie and bowtie2 | |
| 71 generated alignment files. | |
| 72 | |
| 73 Written by Marius van den Beek, m.vandenbeek at gmail . com | |
| 74 </help> | |
| 42 </tool> | 75 </tool> |