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annotate align_families.xml @ 10:ffd06de5cea9 draft

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author nick
date Mon, 23 Nov 2015 21:54:28 -0500
parents f6f61b363467
children 678dd4b4b4e7
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1 <?xml version="1.0"?>
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2 <tool id="align_families" name="Align families" version="0.1">
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3 <description>from duplex sequencing data</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="0.1">duplex</requirement>
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7 <requirement type="set_environment">DUPLEX_DIR</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">python \$DUPLEX_DIR/align_families.py $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 <help>
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28
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29 **What it does**
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30
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31 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.
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32
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33 -----
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34
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35 **Input**
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36
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37 This expects the output format of the "Make families" tool.
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38
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39 -----
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40
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41 **Output**
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42
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43 The output is a tabular file where each line corresponds to a (single) read.
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44
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45 The columns are::
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46
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47 1: barcode (both tags)
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48 2: tag order in barcode ("ab" or "ba")
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49 3: read mate ("1" or "2")
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50 4: read name
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51 5: read sequence, aligned ("-" for gaps)
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52 6: read quality scores, aligned (" " for gaps)
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53
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54 -----
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55
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56 **Alignments**
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57
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58 The alignments are done using MAFFT, specifically the command
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59 ::
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60
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61 $ mafft --nuc --quiet family.fa &gt; family.aligned.fa
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62
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63 </help>
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64 </tool>