Mercurial > repos > matthias > dada2_makesequencetable

annotate dada2_makeSequenceTable.xml @ 9:6da167015b3e draft

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author matthias
date Tue, 28 May 2019 12:19:29 -0400
parents ec4a183cc713
children 31e8d1265580
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1 <tool id="dada2_makeSequenceTable" name="dada2: makeSequenceTable" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>construct a sequence table (analogous to OTU table)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '$dada2_script'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="dada2_script"><![CDATA[
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13 @READ_FOO@
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14 @WRITE_FOO@
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16 library(dada2, quietly=T)
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17 #if $plot == "yes"
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18 library(ggplot2, quietly=T)
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19 #end if
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21 samples <- list()
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22 #for $s in $samples:
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23 samples[["$s.element_identifier"]] <- readRDS('$s')
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24 #end for
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26 seqtab <- makeSequenceTable(samples, orderBy = "$orderBy")
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27
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28 reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
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29 df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)
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30
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31 #if $plot == "yes"
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32 pdf( '$plot_output' )
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33 ggplot(data=df, aes(x=length, y=count)) +
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34 geom_col() +
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35 #if $filter_cond.filter_select != "no"
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36 geom_vline( xintercept=c($filter_cond.min-0.5, $filter_cond.max+0.5) ) +
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37 #end if
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38 theme_bw()
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39 bequiet <- dev.off()
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40 #end if
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41
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42 ## filter by seqlengths
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43 #if $filter_cond.filter_select != "no"
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44 seqtab <- seqtab[, nchar(colnames(seqtab)) %in% seq($filter_cond.min, $filter_cond.max), drop=F]
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45 #end if
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46 write.data( seqtab, '$stable', "dada2_sequencetable" )
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47 ]]></configfile>
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48 </configfiles>
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49 <inputs>
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50 <param argument="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
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51 <param argument="orderBy" type="select" label="Column order">
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52 <option value="abundance">abundance</option>
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53 <option value="nsamples">nsamples</option>
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54 </param>
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55 <conditional name="filter_cond">
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56 <param name="filter_select" type="select" label="Length filter method">
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57 <option value="no">No filter</option>
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58 <option value="minmax">Specify minimum and maximum sequence lengths</option>
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59 </param>
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60 <when value="no"/>
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61 <when value="minmax">
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62 <param name="min" type="integer" value="" label="Minimum sequence length"/>
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63 <param name="max" type="integer" value="" label="Maximum sequence length"/>
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64 </when>
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65 </conditional>
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66 <param name="plot" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="plot sequence length distribution" />
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67 </inputs>
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68 <outputs>
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69 <data name="stable" format="dada2_sequencetable" label="${tool.name} on ${on_string}"/>
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70 <data name="plot_output" format="pdf" label="${tool.name} on ${on_string}: sequence length distribution">
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71 <filter>plot</filter>
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72 </data>
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73 </outputs>
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74 <tests>
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75 <test expect_num_outputs="2">
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76 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
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77 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
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78 <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" />
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79 </test>
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80 <test expect_num_outputs="1">
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81 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
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82 <param name="filter_cond|filter_select" value="minmax"/>
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83 <param name="filter_cond|min" value="200"/>
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84 <param name="filter_cond|max" value="300"/>
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85 <param name="plot" value="no" />
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86 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
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87 </test>
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88 </tests>
0
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89 <help><![CDATA[
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90 Description
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91 ...........
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92
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93 This function constructs a sequence table -- more precisely an amplicon sequence variant table (ASV) table -- a higher-resolution version of the OTU table produced by traditional methods.
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94
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95 The sequence table is a matrix with rows corresponding to (and named by) the samples, and columns corresponding to (and named by) the sequence variants.
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96
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97 Usage
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98 .....
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99
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100 **Input**: The result of derepFastq, dada, or mergePairs.
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101
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102 **Output**: A data set of type dada2_sequencetable, i.e. a tabular with a row for each sample, and a column for each unique sequence across all the samples. The columns are named by the sequence.
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103
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104 Details
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105 .......
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106
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107 Sequences that are much longer or shorter than expected may be the result of non-specific priming. You can remove non-target-length by applying a length filter. This is analogous to “cutting a band” in-silico to get amplicons of the targeted length.
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108
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109 @HELP_OVERVIEW@
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110 ]]></help>
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111 <expand macro="citations"/>
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112 </tool>