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author matthias
date Tue, 15 Oct 2019 07:25:03 -0400
parents 4861220ec0c9
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1 <tool id="dada2_derepFastq" name="dada2: derepFastq" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
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2 <description>dereplicate amplicon sequences</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="stdio"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$dada2_script'
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="dada2_script"><![CDATA[
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14 library(dada2, quietly=T)
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15 derep <- derepFastq('$fls')
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17 ## write.table(derep\$uniques, file = '$derep', quote = F, sep = "\t", row.names = T, col.names = F)
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18 saveRDS(derep, file='$derep')
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19 ]]></configfile>
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20 </configfiles>
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21 <inputs>
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22 <param argument="fls" type="data" format="fastq,fastq.gz" label="Short read data" />
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23 </inputs>
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24 <outputs>
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25 <data name="derep" format="dada2_derep" label="${tool.name} on ${on_string}"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
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30 <output name="derep" value="derepFastq_F3D0_R1.Rdata" ftype="dada2_derep" />
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31 </test>
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32 <!-- test for creating input for dada results for reverse, not needed for testing -->
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33 <test>
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34 <param name="fls" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
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35 <output name="derep" value="derepFastq_F3D0_R2.Rdata" ftype="dada2_derep" />
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 Description
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40 ...........
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41
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42 Dereplication combines all identical sequencing reads into into “unique sequences” with a corresponding “abundance” equal to the number of reads with that unique sequence. Dereplication substantially reduces computation time of the subsequent steps by eliminating redundant comparisons.
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44 Usage
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45 .....
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46
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47 **Input** is a FASTQ dataset containing the filtered and trimmed reads of a sample.
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49 **Output** a dataset with type *dada2_derep* (which is a RData file containing the output of dada2's derepFastq function).
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51 The output can be used as input for the *dada2: dada* tool which infers the sample composition from the dereplicated sequences given an error model.
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53 Details
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54 .......
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56 Dereplication in the DADA2 pipeline has one crucial addition from other pipelines: DADA2 retains a summary of the quality information associated with each unique sequence. The consensus quality profile of a unique sequence is the average of the positional qualities from the dereplicated reads. These quality profiles inform the error model of the subsequent sample inference step, significantly increasing DADA2’s accuracy.
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58 @HELP_OVERVIEW@
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59 ]]></help>
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60 <expand macro="citations"/>
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61 </tool>