Mercurial > repos > mvdbeek > mismatch_frequencies
comparison mismatch_frequencies.xml @ 1:1609cb745999
Uploaded
| author | mvdbeek |
|---|---|
| date | Tue, 27 Jan 2015 05:56:10 -0500 |
| parents | |
| children | edae148b2dd4 |
comparison
equal
deleted
inserted
replaced
| 0:e8ebe5132737 | 1:1609cb745999 |
|---|---|
| 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.3" hidden="false" > | |
| 2 <description>Analyze mismatch frequencies in BAM/SAM alignments</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.7.7">pysam</requirement> | |
| 5 <requirement type="package" version="0.14">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"> | |
| 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."/> | |
| 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="pdf" name="output_pdf" /> | |
| 33 <data format="tabular" name="output_tab" /> | |
| 34 </outputs> | |
| 35 | |
| 36 </tool> |