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annotate duplex.xml @ 0:d2e46adc199e draft

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date Mon, 23 Nov 2015 22:06:21 -0500
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1 <?xml version="1.0"?>
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2 <tool id="duplex" name="Make consensus reads" 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="0.1">duplex</requirement>
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6 <requirement type="set_environment">DUPLEX_DIR</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 python \$DUPLEX_DIR/duplex.py -r $min_reads -q $qual_thres -F $qual_format $input
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10 #if $keep_sscs:
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11 --sscs-file $sscs
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12 #end if
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13 > duplex.fa
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14 && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1
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15 && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name="input" type="data" format="tabular" label="Aligned input reads" />
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20 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
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21 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
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22 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
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23 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
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24 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
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25 </param>
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26 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences" />
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27 </inputs>
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28 <outputs>
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29 <data name="output1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
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30 <data name="output2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
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31 <data name="sscs" format="fasta" label="$tool.name on $on_string (SSCS)">
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32 <filter>keep_sscs</filter>
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33 </data>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input" value="families.msa.tsv"/>
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38 <output name="output1" file="families.cons_1.fa"/>
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39 <output name="output2" file="families.cons_2.fa"/>
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40 </test>
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41 </tests>
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42 <help>
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43
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44 **What it does**
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45
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46 This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.
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47
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48 -----
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49
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50 **Input**
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51
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52 This expects the output format of the "Align families" tool.
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53
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54 -----
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55
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56 **Output**
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57
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58 This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file.
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59
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60 </help>
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61 </tool>