Mercurial > repos > mvdbeek > mismatch_frequencies
comparison mismatch_frequencies.xml @ 2:2974c382105c draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mismatch_frequencies commit 10a7e3877c2568d9c23de53fc97dc1c902ff0524-dirty
author | mvdbeek |
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date | Sat, 22 Dec 2018 04:15:47 -0500 |
parents | 3613460e891e |
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1:3613460e891e | 2:2974c382105c |
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1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.1.0" hidden="false" > | 1 <tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.1.0" 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="0.8.3">pysam</requirement> |
5 <requirement type="package" version="0.14.1">pandas</requirement> | 5 <requirement type="package" version="0.19.0">pandas</requirement> |
6 <requirement type="package" version="1.2.1">matplotlib</requirement> | 6 <requirement type="package" version="1.5.3">matplotlib</requirement> |
7 </requirements> | 7 </requirements> |
8 <command interpreter="python">mismatch_frequencies.py --input | 8 <command detect_errors="aggressive"><![CDATA[ |
9 #for i in $rep | 9 python '$__tool_directory__'/mismatch_frequencies.py --input |
10 "$i.input_file" | 10 #for i in $rep |
11 #end for | 11 "$i.input_file" |
12 --name | 12 #end for |
13 #for i in $rep | 13 --name |
14 "$i.input_file.element_identifier" | 14 #for i in $rep |
15 #end for | 15 "$i.input_file.element_identifier" |
16 --output_pdf $output_pdf --output_tab $output_tab --min $min_length --max $max_length | 16 #end for |
17 --n_mm $number_of_mismatches | 17 --output_pdf '$output_pdf' |
18 --five_p $five_p | 18 --output_tab '$output_tab' |
19 --three_p $three_p | 19 --min $min_length |
20 --expanded_output_tab $expanded_tab | 20 --max $max_length |
21 --possible_mismatches $possible_mismatches | 21 --n_mm $number_of_mismatches |
22 </command> | 22 --five_p $five_p |
23 --three_p $three_p | |
24 --expanded_output_tab '$expanded_tab' | |
25 --possible_mismatches $possible_mismatches | |
26 ]]></command> | |
23 <inputs> | 27 <inputs> |
24 <repeat name="rep" title="alignment files"> | 28 <repeat name="rep" title="alignment files"> |
25 <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which to analyze the mismatches."/> | 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."/> |
26 </repeat> | 30 </repeat> |
27 <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"/> | 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"/> |
31 <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/> | 35 <param name="min_length" label="Minumum read length to analyse" type="integer" value="21"/> |
32 <param name="max_length" label="Maximum read length to analyse" type="integer" value="21"/> | 36 <param name="max_length" label="Maximum read length to analyse" type="integer" value="21"/> |
33 <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/> | 37 <param name="five_p" label="Ignore mismatches in the first N nucleotides of a read" type="integer" value="0"/> |
34 <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"/> | 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"/> |
35 <param help="Output expanded tabular format" label="Nucleotide mismatches per reference sequence" name="expanded" type="select"> | 39 <param help="Output expanded tabular format" label="Nucleotide mismatches per reference sequence" name="expanded" type="select"> |
36 <option select="true" value="false">No</option> | 40 <option selected="true" value="false">No</option> |
37 <option value="expanded">Yes</option> | 41 <option value="expanded">Yes</option> |
38 </param> | 42 </param> |
39 </inputs> | 43 </inputs> |
40 <outputs> | 44 <outputs> |
41 <data format="tabular" name="output_tab" /> | 45 <data format="tabular" name="output_tab" /> |
64 .. class:: infomark | 68 .. class:: infomark |
65 | 69 |
66 | 70 |
67 ***What it does*** | 71 ***What it does*** |
68 | 72 |
69 This tool reconstitues for each aligned read of an alignment file in SAM/BAM format whether | 73 This tool reconstitues for each aligned read of an alignment file in SAM/BAM |
70 a mismatch is annotated in the MD tag, and if that is the case counts the identity of the | 74 format whether a mismatch is annotated in the MD tag, and if that is the case |
71 mismatch relative to the reference sequence. The output is a PDF document with the calculated | 75 counts the identity of the mismatch relative to the reference sequence. The |
72 frequency for each mismatch that occured relative to the total number of valid reads and a table | 76 output is a PDF document with the calculated frequency for each mismatch that |
73 with the corresponding values. Read length can be limited to a specific read length, and 5 prime and | 77 occured relative to the total number of valid reads and a table with the |
74 3 prime-most nucleotides of a read can be ignored. | 78 corresponding values. Read length can be limited to a specific read length, and |
79 5 prime and 3 prime-most nucleotides of a read can be ignored. | |
75 | 80 |
76 ---- | 81 ---- |
77 | 82 |
78 .. class:: warningmark | 83 .. class:: warningmark |
79 | 84 |