Mercurial > repos > nick > dunovo
annotate align_families.xml @ 14:4be10cb5c26e draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
author | nick |
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date | Mon, 11 Sep 2017 16:49:53 -0400 |
parents | ffbdaa57d4c6 |
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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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4be10cb5c26e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
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2 <tool id="align_families" name="Du Novo: Align families" version="0.8.1"> |
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548c63893c70
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3 <description>of duplex sequencing reads</description> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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4 <requirements> |
548c63893c70
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5 <requirement type="package" version="7.221">mafft</requirement> |
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6 <requirement type="package" version="0.8.1">dunovo</requirement> |
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7 <!-- TODO: require Python 2.7 --> |
548c63893c70
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8 </requirements> |
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9 <command detect_errors="exit_code">align_families.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' > '$output' |
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10 </command> |
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11 <inputs> |
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12 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> |
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13 <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send anonymous usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time taken to process it, and the IP address of the machine running it. No parameters or filenames are sent."/> |
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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14 </inputs> |
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15 <outputs> |
548c63893c70
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16 <data name="output" format="tabular"/> |
548c63893c70
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17 </outputs> |
548c63893c70
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18 <tests> |
548c63893c70
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19 <test> |
548c63893c70
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20 <param name="input" value="smoke.families.tsv"/> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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21 <output name="output" file="smoke.families.aligned.tsv"/> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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22 </test> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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23 <test> |
548c63893c70
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24 <param name="input" value="families.in.tsv"/> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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25 <output name="output" file="families.sort.tsv"/> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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26 </test> |
548c63893c70
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27 </tests> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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28 <citations> |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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29 <citation type="bibtex">@article{Stoler2016, |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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30 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton}, |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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31 doi = {10.1186/s13059-016-1039-4}, |
548c63893c70
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32 issn = {1474-760X}, |
548c63893c70
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33 journal = {Genome biology}, |
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34 number = {1}, |
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35 pages = {180}, |
548c63893c70
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36 pmid = {27566673}, |
548c63893c70
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37 publisher = {Genome Biology}, |
548c63893c70
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38 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}}, |
548c63893c70
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39 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673}, |
548c63893c70
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fcd6f371638bc29da6dbe22f939f7a5a7f360481\n'-dirty
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40 volume = {17}, |
548c63893c70
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41 year = {2016} |
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42 }</citation> |
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43 </citations> |
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44 <help> |
548c63893c70
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45 |
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46 **What it does** |
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47 |
548c63893c70
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48 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads. |
548c63893c70
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49 |
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50 ----- |
548c63893c70
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51 |
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52 **Input** |
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53 |
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54 This expects the output format of the "Make families" tool. |
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55 |
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56 ----- |
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57 |
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58 **Output** |
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59 |
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60 The output is a tabular file where each line corresponds to a (single) read. |
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61 |
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62 The columns are:: |
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63 |
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64 1: barcode (both tags) |
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65 2: tag order in barcode ("ab" or "ba") |
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66 3: read mate ("1" or "2") |
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67 4: read name |
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68 5: read sequence, aligned ("-" for gaps) |
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69 6: read quality scores, aligned (" " for gaps) |
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70 |
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71 ----- |
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72 |
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73 **Alignments** |
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74 |
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75 The alignments are done using MAFFT, specifically the command |
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76 :: |
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77 |
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78 $ mafft --nuc --quiet family.fa > family.aligned.fa |
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79 |
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80 </help> |
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81 </tool> |