--- a/dada2_mergePairs.xml	Tue Apr 09 07:07:52 2019 -0400
+++ b/dada2_mergePairs.xml	Mon Apr 29 08:59:27 2019 -0400
@@ -12,18 +12,18 @@
         <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"))
+dadaF <- readRDS('$dadaf')
+dadaR <- readRDS('$dadar')
+derepF <- readRDS('$derepf')
+derepR <- readRDS('$derepr')
 
-merged <- mergePairs(dadaF, derepF, dadaR, derepR, minOverlap = $minoverlap, maxMismatch = $maxmismatch,
+merged <- mergePairs(dadaF, derepF, dadaR, derepR, minOverlap = $minOverlap, maxMismatch = $maxMismatch,
     returnRejects = FALSE, propagateCol = character(0),
-    justConcatenate = $justconcatenate, trimOverhang = $trimoverhang)
+    justConcatenate = $justConcatenate, trimOverhang = $trimOverhang)
 
-##saveRDS(merged, file='$merged')
+saveRDS(merged, file='$merged')
 ##For display in Galaxy this could be transposed (..but the user could also do it herself)
-write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T)
+##write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T)
     ]]></configfile>
     </configfiles>
     <inputs>
@@ -31,20 +31,47 @@
         <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" help="The forward and reverse-complemented reverse read are concatenated rather than merged, with a 10 Ns spacer inserted between them"/>
-        <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"/>
+        <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"/>
     </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"/>
+            <output name="merged" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs" />
+        </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 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 sefault) or which contain too many (>0 by default) mismatches in the overlap region.
+
+Usage
+.....
+
+**Input**
+
+- dereplicated reads and learned error rates of the forward reads
+- dereplicated reads and learned error rates of the reversereads
+
+**Output**
+
+- a data set of type dada2_mergepairs (which is a RData file containing the output of dada2's mergePairs function).
+
+Details
+.......
+
+@HELP_OVERVIEW@
+
+
     ]]></help>
     <expand macro="citations"/>
 </tool>