Mercurial > repos > matthias > dada2_makesequencetable

annotate dada2_makeSequenceTable.xml @ 3:c3834c230b0a draft

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author matthias
date Mon, 29 Apr 2019 09:00:48 -0400
parents d2e7c5f8a9f7
children ec4a183cc713
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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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15 library(dada2, quietly=T)
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16 #if $plot == "yes"
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17 library(ggplot2, quietly=T)
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18 #end if
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20 samples <- list()
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21 #for $s in $samples:
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22 #if $len($samples) == 1
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23 samples <- readRDS('$s')
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24 #else
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25 samples[["$s.element_identifier"]] <- readRDS('$s')
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26 #end if
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27 #end for
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28 ## make sequence table
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29 seqtab <- makeSequenceTable(samples, orderBy = "$orderBy")
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30
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32 reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
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33 df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)
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34
2
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35 #if $plot == "yes"
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36 pdf( '$plot_output' )
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37 ggplot(data=df, aes(x=length, y=count)) +
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38 geom_col() +
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39 #if $filter_cond.filter_select != "no"
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40 geom_vline( xintercept=c($filter_cond.min-0.5, $filter_cond.max+0.5) ) +
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41 #end if
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42 theme_bw()
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43 bequiet <- dev.off()
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44 #end if
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45
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46 ## filter by seqlengths
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47 #if $filter_cond.filter_select != "no"
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48 seqtab <- seqtab[, nchar(colnames(seqtab)) %in% seq($filter_cond.min, $filter_cond.max)]
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49 #end if
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50
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51 write.table(seqtab, "$stable", quote=F, sep="\t", row.names = T, col.names = NA)
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52 ]]></configfile>
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53 </configfiles>
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54 <inputs>
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55 <param name="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
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56 <param argument="orderBy" type="select" label="Column order">
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57 <option value="abundance">abundance</option>
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58 <option value="nsamples">nsamples</option>
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59 </param>
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60 <conditional name="filter_cond">
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61 <param name="filter_select" type="select" label="Length filter method">
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62 <option value="no">No filter</option>
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63 <option value="minmax">Specify minimum and maximum sequence lengths</option>
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64 </param>
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65 <when value="no"/>
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66 <when value="minmax">
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67 <param name="min" type="integer" value="" label="Minimum sequence length"/>
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68 <param name="max" type="integer" value="" label="Maximum sequence length"/>
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69 </when>
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70 </conditional>
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71 <param name="plot" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="plot sequence length distribution" />
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72 </inputs>
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73 <outputs>
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74 <data name="stable" format="dada2_sequencetable" label="${tool.name} on ${on_string}"/>
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75 <data name="plot_output" format="pdf" label="${tool.name} on ${on_string}: sequence length distribution">
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76 <filter>plot</filter>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
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82 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
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83 </test>
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84 </tests>
0
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85 <help><![CDATA[
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86 Description
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87 ...........
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88
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89 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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90
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91 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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92
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93 Usage
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94 .....
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95
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96 **Input**: The result of derepFastq, dada, or mergePairs.
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97
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98 **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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99
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100 Details
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101 .......
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102
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103 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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104
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105 @HELP_OVERVIEW@
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106 ]]></help>
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107 <expand macro="citations"/>
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108 </tool>