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annotate macros.xml @ 5:caa2bdb8a431 draft

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author matthias
date Sun, 05 May 2019 12:39:41 -0400
parents c3315e7a6130
children 9f32a9f91411
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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" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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16 ]]></version_command>
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17 </xml>
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19 <xml name="citations">
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20 <citations>
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21 <citation type="doi">10.1038/nmeth.3869</citation>
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22 <yield/>
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23 </citations>
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24 </xml>
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25
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26 <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
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27
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28 <!-- function to read dada2 data types
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29 - derep, dada, and mergepairs are simply read as RDS
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30 - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
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31 - uniques is a named integer vector (columns=ASVs, only one rows)-->
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32 <token name="@READ_FOO@"><![CDATA[
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33 read.uniques <- function ( fname ) {
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34 p <- read.table(fname, header=F, sep="\t")
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35 n <-x[,2]
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36 names(n)<-x[,1]
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37 }
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38 #def read_data($dataset)
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39 #if $dataset.is_of_type('dada2_sequencetable')
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40 t(as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) ))
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41 #else if $dataset.is_of_type('dada2_uniques')
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42 read.uniques('$dataset')
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43 #else if $dataset.is_of_type('tabular')
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44 read.table('$dataset', header=T, sep="\t", row.names=1)
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45 #else
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46 readRDS('$dataset')
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47 #end if
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48 #end def
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49 ]]></token>
5
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50 <!-- function to write dada2 data types (the content or the R variable 'out' is written)
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51 - derep, dada, and mergepairs are written as RDS
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52 - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
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53 - uniques is a named integer vector (columns=ASVs, only one rows)-->
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54 <token name="@WRITE_FOO@"><![CDATA[
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55 write.data <- function( data, fname, type ){
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56 if( type == 'dada2_uniques'){
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57 write.table(data, file = fname, quote = F, sep = "\t", row.names = T, col.names = F)
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58 }else if( type== 'dada2_sequencetable'){
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59 write.table(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA)
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60 }else{
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61 saveRDS(data, file=fname)
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62 }
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63 }
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64 ]]></token>
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65
3
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66 <!-- for filterAndTrim -->
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67 <xml name="trimmers">
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68 <section name="trim" title="Trimming parameters">
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69 <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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70 <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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71 <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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72 <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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73 </section>
0
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74 </xml>
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75 <xml name="filters">
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76 <section name="filter" title="Filtering parameters">
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77 <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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78 <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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79 <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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80 <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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81 <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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82 </section>
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83 </xml>
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84
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85 <xml name="errorEstimationFunction">
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86 <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function">
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87 <option value="loessErrfun">loess: Use a loess fit to estimate error rates from transition counts</option>
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88 <option value="noqualErrfun">noqual: Estimate error rates for each type of transition while ignoring quality scores.</option>
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89 <option value="PacBioErrfun">PacBio: Estimate error rates from transition counts in PacBio CCS data.</option>
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90 </param>
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91 </xml>
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92 <token name="@HELP_OVERVIEW@"><![CDATA[
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93 Overview
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94 ........
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95
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96 The intended use of the dada2 tools for paired sequencing data is shown in the following image.
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97
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98 .. image:: pairpipe.png
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99
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100 For single end data you the steps "Unzip collection" and "mergePairs" are not necessary.
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101
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102 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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103 ]]></token>
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104 </macros>