--- a/dada2_mergePairs.xml	Mon Apr 29 09:51:19 2019 -0400
+++ b/dada2_mergePairs.xml	Sun May 05 12:32:30 2019 -0400
@@ -12,13 +12,13 @@
         <configfile name="dada2_script"><![CDATA[
 library(dada2, quietly=T)
 
-dadaF <- readRDS('$dadaf')
-dadaR <- readRDS('$dadar')
-derepF <- readRDS('$derepf')
-derepR <- readRDS('$derepr')
+dadaF <- readRDS('$dadaF')
+dadaR <- readRDS('$dadaR')
+derepF <- readRDS('$derepF')
+derepR <- readRDS('$derepR')
 
 merged <- mergePairs(dadaF, derepF, dadaR, derepR, minOverlap = $minOverlap, maxMismatch = $maxMismatch,
-    returnRejects = FALSE, propagateCol = character(0),
+## currently not accessible by the wrapper    returnRejects = FALSE, propagateCol = character(0),
     justConcatenate = $justConcatenate, trimOverhang = $trimOverhang)
 
 saveRDS(merged, file='$merged')
@@ -27,32 +27,44 @@
     ]]></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 argument="dadaF" type="data" format="dada2_dada" label="Dada results for forward reads"/>
+        <param argument="derepF" type="data" format="dada2_derep" label="Dereplicated forward reads"/>
+        <param argument="dadaR" type="data" format="dada2_dada" label="Dada results for reverse reads"/>
+        <param argument="derepR" type="data" format="dada2_derep" label="Dereplicated reverse reads"/>
         <param argument="minOverlap" type="integer" value="12" min="0" label="Minimum length of the overlap"/>
         <param argument="maxMismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/>
-        <param argument="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"/>
-        <param argument="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"/>
+        <param argument="justConcatenate" type="boolean" checked="false" truevalue="TRUE" 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"/>
+        <param argument="trimOverhang" type="boolean" checked="false" truevalue="TRUE" 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"/>
     </inputs>
     <outputs>
         <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
         <test>
-            <param name="dadaf" ftype="dada2_dada" value="dada_F3D0_R1.Rdata"/>
-            <param name="derepf" ftype="dada2_derep" value="derepFastq_F3D0_R1.Rdata"/>
-            <param name="dadar" ftype="dada2_dada" value="dada_F3D0_R2.Rdata"/>
-            <param name="derepr" ftype="dada2_derep" value="derepFastq_F3D0_R2.Rdata"/>
+            <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_R1.Rdata"/>
+            <param name="derepF" ftype="dada2_derep" value="derepFastq_F3D0_R1.Rdata"/>
+            <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_R2.Rdata"/>
+            <param name="derepR" ftype="dada2_derep" value="derepFastq_F3D0_R2.Rdata"/>
             <output name="merged" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs" />
         </test>
+        <!-- test non-default options -->
+        <test>
+            <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_R1.Rdata"/>
+            <param name="derepF" ftype="dada2_derep" value="derepFastq_F3D0_R1.Rdata"/>
+            <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_R2.Rdata"/>
+            <param name="derepR" ftype="dada2_derep" value="derepFastq_F3D0_R2.Rdata"/>
+            <output name="merged" value="mergePairs_F3D0_nondefault.Rdata" ftype="dada2_mergepairs" />
+            <param name="minOverlap" value="8" />
+            <param name="maxMismatch" value="1"/>
+            <param name="justConcatenate" value="TRUE" />
+            <param name="trimOverhang" value="TRUE" />
+        </test>
     </tests>
     <help><![CDATA[
 Description
 ...........
 
-This function attempts to merge each denoised pair of forward and reverse reads, rejecting any pairs which do not sufficiently overlap (at least 12bp by sefault) or which contain too many (>0 by default) mismatches in the overlap region.
+This function attempts to merge each denoised pair of forward and reverse reads, rejecting any pairs which do not sufficiently overlap (at least 12bp by default) or which contain too many (>0 by default) mismatches in the overlap region.
 
 Usage
 .....
@@ -60,7 +72,7 @@
 **Input**
 
 - dereplicated reads and learned error rates of the forward reads
-- dereplicated reads and learned error rates of the reversereads
+- dereplicated reads and learned error rates of the reverse reads
 
 **Output**