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author matthias
date Tue, 09 Apr 2019 07:07:52 -0400
parents 44230c777694
children caae353b2928
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1 <tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>Merge denoised forward and reverse reads</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 '$dada2_script'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="dada2_script"><![CDATA[
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13 library(dada2, quietly=T)
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15 dadaF <- readRDS(file.path('$dadaf'))
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16 dadaR <- readRDS(file.path('$dadar'))
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17 derepF <- readRDS(file.path('$derepf.extra_files_path',"Rdata"))
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18 derepR <- readRDS(file.path('$derepr.extra_files_path',"Rdata"))
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20 merged <- mergePairs(dadaF, derepF, dadaR, derepR, minOverlap = $minoverlap, maxMismatch = $maxmismatch,
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21 returnRejects = FALSE, propagateCol = character(0),
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22 justConcatenate = $justconcatenate, trimOverhang = $trimoverhang)
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24 ##saveRDS(merged, file='$merged')
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25 ##For display in Galaxy this could be transposed (..but the user could also do it herself)
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26 write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T)
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27 ]]></configfile>
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28 </configfiles>
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29 <inputs>
2
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30 <param name="dadaf" type="data" format="dada2_dada" label="Dada results for forward reads"/>
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31 <param name="derepf" type="data" format="dada2_derep" label="Dereplicated forward reads"/>
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32 <param name="dadar" type="data" format="dada2_dada" label="Dada results for reverse reads"/>
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33 <param name="derepr" type="data" format="dada2_derep" label="Dereplicated reverse reads"/>
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34 <param name="minoverlap" type="integer" value="12" min="0" label="Minimum length of the overlap"/>
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35 <param name="maxmismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/>
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36 <param name="justconcatenate" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="Concatenated rather than merge" help="The forward and reverse-complemented reverse read are concatenated rather than merged, with a 10 Ns spacer inserted between them"/>
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37 <param name="trimoverhang" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="Trim overhangs" help="Overhangs are when the reverse read extends past the start of the forward read, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region"/>
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38 </inputs>
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39 <outputs>
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40 <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/>
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41 </outputs>
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42
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43 <help><![CDATA[
2
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44 Description
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45 ...........
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46
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47 This function attempts to merge each denoised pair of forward and reverse reads, rejecting any pairs which do not sufficiently overlap or which contain too many (>0 by default) mismatches in the overlap region.
0
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48 ]]></help>
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49 <expand macro="citations"/>
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50 </tool>