Mercurial > repos > mvdbeek > mismatch_frequencies
comparison mismatch_frequencies.xml @ 6:a7bf987b8cc4
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| author | mvdbeek |
|---|---|
| date | Tue, 27 Jan 2015 12:30:07 -0500 |
| parents | |
| children | 270681625775 |
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| 5:e554c1973398 | 6:a7bf987b8cc4 |
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| 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.4" 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="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_s2.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 <output name="pdf" file="mismatch.pdf" ftype="pdf"/> | |
| 44 </test> | |
| 45 </tests> | |
| 46 </tool> |