--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dada2_mergePairs.xml	Fri Mar 08 06:39:56 2019 -0500
@@ -0,0 +1,47 @@
+<tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@">
+    <description>Merge denoised forward and reverse reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript '$dada2_script'
+    ]]></command>
+    <configfiles>
+        <configfile name="dada2_script"><![CDATA[
+library(dada2, quietly=T)
+
+dadaF <- readRDS(file.path('$dadaf'))
+dadaR <- readRDS(file.path('$dadar'))
+derepF <- readRDS(file.path('$derepf.extra_files_path',"Rdata"))
+derepR <- readRDS(file.path('$derepr.extra_files_path',"Rdata"))
+
+merged <- mergePairs(dadaF, derepF, dadaR, derepR, minOverlap = $minoverlap, maxMismatch = $maxmismatch,
+    returnRejects = FALSE, propagateCol = character(0),
+    justConcatenate = $justconcatenate, trimOverhang = $trimoverhang)
+
+##saveRDS(merged, file='$merged')
+##For display in Galaxy this could be transposed (..but the user could also do it herself)
+write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T)
+    ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="dadaf" type="data" format="dada2_dada" label="dada results for forward reads"/>
+        <param name="derepf" type="data" format="dada2_derep" label="dereplicated forward reads"/>
+        <param name="dadar" type="data" format="dada2_dada" label="dada results for reverse reads"/>
+        <param name="derepr" type="data" format="dada2_derep" label="dereplicated reverse reads"/>
+        <param name="minoverlap" type="integer" value="12" min="0" label="minimum length of the overlap"/>
+        <param name="maxmismatch" type="integer" value="0" min="0" label="maximum number of mismatches"/>
+        <param name="justconcatenate" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="concatenated rather than merge"/>
+        <param name="trimoverhang" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="trim overhangs"/>
+    </inputs>
+    <outputs>
+        <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/>
+    </outputs>
+
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>