Mercurial > repos > nick > dunovo
annotate make_families.xml @ 21:f509cd1d5a78 draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty
author | nick |
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date | Thu, 04 Jan 2018 23:55:06 -0500 |
parents | e5d1d90c099b |
children | db602e459536 |
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548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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1 <?xml version="1.0"?> |
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f509cd1d5a78
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty
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2 <tool id="make_families" name="Du Novo: Make families" version="2.0.10"> |
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548c63893c70
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3 <description>of duplex sequencing reads</description> |
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4 <requirements> |
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f509cd1d5a78
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5 <requirement type="package" version="2.0.10">dunovo</requirement> |
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6 </requirements> |
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7 <!-- TODO: Add dependency on coreutils to get paste? --> |
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e5d1d90c099b
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8 <version_command>make-consensi.py --version</version_command> |
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9 <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' > '$output' |
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10 </command> |
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11 <inputs> |
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12 <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/> |
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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13 <param name="fastq2" type="data" format="fastq" label="Sequencing reads, mate 2"/> |
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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14 <param name="taglen" type="integer" value="12" min="0" label="Tag length" help="length of each random barcode on the ends of the fragments"/> |
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15 <param name="invariant" type="integer" value="5" min="0" label="Invariant sequence length" help="length of the sequence between the tag and actual sample sequence (the restriction site, normally)"/> |
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16 </inputs> |
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17 <outputs> |
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18 <data name="output" format="tabular"/> |
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19 </outputs> |
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20 <tests> |
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21 <test> |
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22 <param name="fastq1" value="smoke_1.fq"/> |
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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23 <param name="fastq2" value="smoke_2.fq"/> |
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24 <param name="taglen" value="5"/> |
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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25 <param name="invariant" value="1"/> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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26 <output name="output" file="smoke.families.tsv"/> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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27 </test> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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28 <test> |
548c63893c70
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29 <param name="fastq1" value="smoke_1.fq"/> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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30 <param name="fastq2" value="smoke_2.fq"/> |
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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31 <param name="taglen" value="5"/> |
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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32 <param name="invariant" value="0"/> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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33 <output name="output" file="smoke.families.i0.tsv"/> |
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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34 </test> |
548c63893c70
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35 </tests> |
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36 <help> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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37 |
548c63893c70
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38 **What it does** |
548c63893c70
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39 |
548c63893c70
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40 This tool is for processing raw duplex sequencing data, removing the barcodes and grouping by them into families of reads from the same fragment. |
548c63893c70
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41 |
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42 ----- |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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43 |
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44 **Output** |
548c63893c70
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45 |
548c63893c70
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46 The output will be a tabular file where each line corresponds to a pair of input reads. |
548c63893c70
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47 |
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48 The columns are:: |
548c63893c70
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49 |
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50 1: barcode (both tags joined and ordered) |
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51 2: tag order in barcode ("ab" or "ba") |
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52 3: read1 name |
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53 4: read1 sequence (minus the tag and invariant sequences) |
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54 5: read1 quality scores (minus the same tag and invariant) |
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55 6: read2 name |
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56 7: read2 sequence (minus the tag and invariant sequences) |
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57 8: read2 quality scores (minus the same tag and invariant) |
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58 |
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59 ----- |
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60 |
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61 **Barcode creation** |
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62 |
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63 For each pair, the tool will remove the tag at the beginning of each read and create a barcode by concatenating the two tags. The order of the tags is determined by a string comparison so that it will make an identical barcode from pairs of either order. The original tag order will be noted in the second column. |
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64 |
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65 Since pairs from opposite strands will have the same tags, but in the reverse order, this produces the same barcode for reads from the same fragment, regardless of strand. Then a simple sort will group all reads from the same strand together, separated into strands by the different "order" values. |
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66 |
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67 Examples:: |
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68 |
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69 +---------------+-----------------+ |
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70 | input tags | output | |
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71 +-------+-------+-------+---------+ |
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72 | read1 | read2 | order | barcode | |
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73 +-------+-------+-------+---------+ |
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74 | ATG | CCT | ab | ATGCCT | |
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75 +-------+-------+-------+---------+ |
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76 | CCT | ATG | ba | ATGCCT | |
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77 +-------+-------+-------+---------+ |
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78 |
15
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79 </help> |
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80 <citations> |
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81 <citation type="bibtex">@article{Stoler2016, |
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82 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton}, |
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83 doi = {10.1186/s13059-016-1039-4}, |
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84 issn = {1474-760X}, |
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85 journal = {Genome biology}, |
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86 number = {1}, |
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87 pages = {180}, |
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88 pmid = {27566673}, |
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89 publisher = {Genome Biology}, |
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90 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}}, |
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91 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673}, |
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92 volume = {17}, |
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93 year = {2016} |
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94 }</citation> |
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95 </citations> |
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96 </tool> |