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annotate align_families.xml @ 4:7f513b9b1b1e draft

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Change names to dunovo, use newer Github release.
author nick
date Mon, 21 Dec 2015 14:47:48 -0500
parents aedbdf8ce1af
children 4bc49a5769ee
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1 <?xml version="1.0"?>
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2 <tool id="align_families" name="Du Novo: Align families" version="0.3">
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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="0.3">duplex</requirement>
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7 <requirement type="set_environment">DUPLEX_DIR</requirement>
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8 <!-- TODO: require Python 2.7 -->
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9 </requirements>
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10 <command detect_errors="exit_code">python \$DUPLEX_DIR/align_families.py -p \${GALAXY_SLOTS:-1} $input &gt; $output
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11 </command>
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12 <inputs>
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13 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
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14 </inputs>
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15 <outputs>
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16 <data name="output" format="tabular"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input" value="smoke.families.tsv"/>
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21 <output name="output" file="smoke.families.aligned.tsv"/>
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22 </test>
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23 <test>
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24 <param name="input" value="families.in.tsv"/>
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25 <output name="output" file="families.sort.tsv"/>
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26 </test>
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27 </tests>
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28 <help>
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29
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30 **What it does**
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31
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32 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.
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33
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34 -----
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35
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36 **Input**
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37
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38 This expects the output format of the "Make families" tool.
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39
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40 -----
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41
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42 **Output**
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43
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44 The output is a tabular file where each line corresponds to a (single) read.
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45
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46 The columns are::
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48 1: barcode (both tags)
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49 2: tag order in barcode ("ab" or "ba")
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50 3: read mate ("1" or "2")
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51 4: read name
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52 5: read sequence, aligned ("-" for gaps)
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53 6: read quality scores, aligned (" " for gaps)
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54
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55 -----
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56
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57 **Alignments**
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58
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59 The alignments are done using MAFFT, specifically the command
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60 ::
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62 $ mafft --nuc --quiet family.fa &gt; family.aligned.fa
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63
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64 </help>
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65 </tool>