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annotate macros.xml @ 4:9f888de151d1 draft

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author matthias
date Mon, 29 Apr 2019 09:48:19 -0400
parents 10141f4eaae9
children 9aeea74a1fc9
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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10 <token name="@DADA2_VERSION@">1.10.0</token>
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11 <token name="@WRAPPER_VERSION@">1</token>
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12
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13 <xml name="version_command">
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14 <version_command><![CDATA[
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15 echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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16 ]]></version_command>
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17 </xml>
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19 <xml name="citations">
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20 <citations>
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21 <citation type="doi">10.1038/nmeth.3869</citation>
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22 <yield/>
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23 </citations>
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24 </xml>
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25
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26 <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
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28 <token name="@READ_FOO@"><![CDATA[
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29 #def read_data($dataset)
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30 #if $dataset.is_of_type('dada2_derep')
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31 readRDS('$dataset)
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32 #else if $dataset.is_of_type('dada2_dada')
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33 readRDS('$dataset')
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34 #else if $dataset.is_of_type('dada2_sequencetable')
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35 as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) )
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36 #else if $dataset.is_of_type('dada2_mergepairs')
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37 readRDS('$dataset')
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38 #else if $dataset.is_of_type('tabular')
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39 read.table('$dataset', header=T, sep="\t", row.names=1 )
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40 #else
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41 #raise Exception("error: unknown input type")
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42 #end if
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43 #end def
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44 ]]></token>
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45 <!-- for filterAndTrim -->
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46 <xml name="trimmers">
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47 <section name="trim" title="Trimming parameters">
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48 <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
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49 <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>
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50 <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
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51 <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded."/>
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52 </section>
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53 </xml>
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54 <xml name="filters">
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55 <section name="filter" title="Filtering parameters">
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56 <param argument="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/>
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57 <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
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58 <param argument="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/>
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59 <param argument="minQ" type="integer" value="0" min="0" label="Remove low quality reads" help="Reads contain a quality score less than this value will be discarded"/>
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60 <param argument="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by number expected errors" help="Reads with a higher number of expected errors (EE) will be discarded, where EE = sum(10^(-Q_i/10)), with Q are the nominal quality scores at the read positions"/>
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61 </section>
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62 </xml>
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63
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64 <xml name="errorEstimationFunction">
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65 <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function">
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66 <option value="loessErrfun">loess</option>
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67 <option value="noqualErrfun">noqual</option>
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68 <option value="PacBioErrfun">PacBio</option>
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69 </param>
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70 </xml>
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71 <token name="@HELP_OVERVIEW@"><![CDATA[
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72 Overview
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73 ........
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75 The intended use of the dada2 tools for paired sequencing data is shown in the following image.
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77 .. image:: pairpipe.png
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79 For single end data you the steps "Unzip collection" and "mergePairs" are not necessary.
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81 More information may be found on the dada2 homepage:: https://benjjneb.github.io/dada2/index.html (in particular tutorials) or the documentation of dada2's R package https://bioconductor.org/packages/release/bioc/html/dada2.html (in particular the pdf which contains the full documentation of all parameters)
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82 ]]></token>
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83 </macros>