Mercurial > repos > matthias > dada2_makesequencetable

annotate dada2_makeSequenceTable.xml @ 0:98e24c66eeb2 draft

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author matthias
date Fri, 08 Mar 2019 06:42:56 -0500
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children d2e7c5f8a9f7
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1 <tool id="dada2_makeSequenceTable" name="dada2: makeSequenceTable" version="@DADA2_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
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15 library(dada2, quietly=T)
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16 #if $filter.plot == "yes"
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17 library(ggplot2, quietly=T)
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18 #end if
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19
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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 <- $read_data($s)
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24 #else
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25 samples[["$s.element_identifier"]] <- $read_data($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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31 ## get and plot length distribution
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32 seqlen <- data.frame(length = nchar(getSequences(seqtab)))
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33 seqlenq <- quantile(seqlen\$length, probs=c( $filter.plower, $filter.pupper ))
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34
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35 #if $filter.plot == "yes"
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36 pdf( '$plot' )
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37 ggplot(seqlen) +
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38 geom_histogram( aes(x=length), binwidth=1 ) +
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39 geom_vline(xintercept=c(seqlenq[1]-0.5, seqlenq[2]+0.5))
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40 bequiet <- dev.off()
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41 #end if
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42
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43 ## filter by seqlengths
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44 #if $filter.filter == "yes"
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45 seqtab <- seqtab[,nchar(colnames(seqtab)) %in% seqlenq]
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46 #end if
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47
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48 write.table(seqtab, "$stable", quote=F, sep="\t", row.names = T, col.names = NA)
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49 ]]></configfile>
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50 </configfiles>
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51 <inputs>
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52 <param name="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
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53 <param name="orderby" type="select" label="Column order">
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54 <option value="abundance">abundance</option>
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55 <option value="nsamples">nsamples</option>
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56 </param>
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57 <section name="filter" title="Plot and filter sequence lengths">
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58 <param name="plower" type="float" min="0" max="1" value="0.01" label="lower quantile" />
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59 <param name="pupper" type="float" min="0" max="1" value="0.99" label="upper quantile" />
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60 <param name="plot" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="plot sequence length distribution" />
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61 <param name="filter" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="filter sequence length using quantiles" />
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62 </section>
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63 </inputs>
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64 <outputs>
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65 <data name="stable" format="dada2_sequencetable" label="${tool.name} on ${on_string}"/>
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66 <data name="plot" format="pdf" label="${tool.name} on ${on_string}: sequence length distribution">
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67 <filter>filter['plot']</filter>
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68 </data>
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69 </outputs>
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70
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71 <help><![CDATA[
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72 TODO: Fill in help.
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73 ]]></help>
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74 <expand macro="citations"/>
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75 </tool>