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annotate align_families.xml @ 0:548c63893c70 draft

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author nick
date Sat, 18 Feb 2017 05:27:09 -0500
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1 <?xml version="1.0"?>
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2 <tool id="align_families" name="Du Novo: Align families" version="0.7">
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3 <description>of duplex sequencing reads</description>
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4 <requirements>
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5 <requirement type="package" version="7.221">mafft</requirement>
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6 <requirement type="package" version="0.7">dunovo</requirement>
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7 <!-- TODO: require Python 2.7 -->
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8 </requirements>
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9 <command detect_errors="exit_code">align_families.py -p \${GALAXY_SLOTS:-1} '$input' &gt; '$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 </inputs>
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14 <outputs>
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15 <data name="output" format="tabular"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input" value="smoke.families.tsv"/>
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20 <output name="output" file="smoke.families.aligned.tsv"/>
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21 </test>
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22 <test>
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23 <param name="input" value="families.in.tsv"/>
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24 <output name="output" file="families.sort.tsv"/>
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25 </test>
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26 </tests>
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27 <citations>
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28 <citation type="bibtex">@article{Stoler2016,
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29 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
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30 doi = {10.1186/s13059-016-1039-4},
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31 issn = {1474-760X},
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32 journal = {Genome biology},
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33 number = {1},
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34 pages = {180},
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35 pmid = {27566673},
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36 publisher = {Genome Biology},
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37 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
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38 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
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39 volume = {17},
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40 year = {2016}
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41 }</citation>
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42 </citations>
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43 <help>
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44
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45 **What it does**
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46
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47 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.
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48
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49 -----
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50
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51 **Input**
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52
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53 This expects the output format of the "Make families" tool.
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54
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55 -----
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57 **Output**
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58
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59 The output is a tabular file where each line corresponds to a (single) read.
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60
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61 The columns are::
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62
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63 1: barcode (both tags)
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64 2: tag order in barcode ("ab" or "ba")
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65 3: read mate ("1" or "2")
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66 4: read name
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67 5: read sequence, aligned ("-" for gaps)
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68 6: read quality scores, aligned (" " for gaps)
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69
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70 -----
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71
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72 **Alignments**
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73
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74 The alignments are done using MAFFT, specifically the command
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75 ::
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76
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77 $ mafft --nuc --quiet family.fa &gt; family.aligned.fa
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78
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79 </help>
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80 </tool>