<?xml version="1.0"?>
<tool id="align_families" name="Du Novo: Align families" version="0.6">
  <description>of duplex sequencing reads</description>
  <requirements>
    <requirement type="package" version="7.221">mafft</requirement>
    <requirement type="package" version="0.6">duplex</requirement>
    <requirement type="set_environment">DUPLEX_DIR</requirement>
    <!-- TODO: require Python 2.7 -->
  </requirements>
  <command detect_errors="exit_code">python "\$DUPLEX_DIR/align_families.py" -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
  </inputs>
  <outputs>
    <data name="output" format="tabular"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="smoke.families.tsv"/>
      <output name="output" file="smoke.families.aligned.tsv"/>
    </test>
    <test>
      <param name="input" value="families.in.tsv"/>
      <output name="output" file="families.sort.tsv"/>
    </test>
  </tests>
  <citations>
    <citation type="bibtex">@article{Stoler2016,
      author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
      doi = {10.1186/s13059-016-1039-4},
      issn = {1474-760X},
      journal = {Genome biology},
      number = {1},
      pages = {180},
      pmid = {27566673},
      publisher = {Genome Biology},
      title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
      url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
      volume = {17},
      year = {2016}
    }</citation>
  </citations>
  <help>

**What it does**

This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.

-----

**Input**

This expects the output format of the "Make families" tool.

-----

**Output**

The output is a tabular file where each line corresponds to a (single) read.

The columns are::

  1: barcode (both tags)
  2: tag order in barcode ("ab" or "ba")
  3: read mate ("1" or "2")
  4: read name
  5: read sequence, aligned ("-" for gaps)
  6: read quality scores, aligned (" " for gaps)

-----

**Alignments**

The alignments are done using MAFFT, specifically the command
::

  $ mafft --nuc --quiet family.fa &gt; family.aligned.fa

    </help>
</tool>