--- a/dada2_derepFastq.xml	Mon Apr 29 09:48:55 2019 -0400
+++ b/dada2_derepFastq.xml	Sun May 05 12:24:18 2019 -0400
@@ -12,26 +12,27 @@
     <configfiles>
         <configfile name="dada2_script"><![CDATA[
 library(dada2, quietly=T)
-derep <- derepFastq('$reads')
+derep <- derepFastq('$fls')
 
 ## write.table(derep\$uniques, file = '$derep', quote = F, sep = "\t", row.names = T, col.names = F)
 saveRDS(derep, file='$derep')
     ]]></configfile>
     </configfiles>
     <inputs>
-        <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data" />
+        <param argument="fls" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data" />
     </inputs>
     <outputs>
         <data name="derep" format="dada2_derep" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
         <test>
-            <param name="reads" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
-            <output name="output" value="derepFastq_F3D0_R1.Rdata" ftype="dada2_derep" />
+            <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
+            <output name="derep" value="derepFastq_F3D0_R1.Rdata" ftype="dada2_derep" />
         </test>
+        <!-- test for creating input for dada results for reverse, not needed for testing -->
         <test>
-            <param name="reads" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
-            <output name="output" value="derepFastq_F3D0_R2.Rdata" ftype="dada2_derep" />
+            <param name="fls" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
+            <output name="derep" value="derepFastq_F3D0_R2.Rdata" ftype="dada2_derep" />
         </test>
     </tests>
     <help><![CDATA[