--- a/dada2_filterAndTrim.xml	Mon Apr 29 09:50:04 2019 -0400
+++ b/dada2_filterAndTrim.xml	Sun May 05 12:28:14 2019 -0400
@@ -79,10 +79,10 @@
                 <option value="FALSE">no</option>
             </param>
             <when value="TRUE">
-                <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired short read data"/>
+                <param name="reads" argument="fwd/rev" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired short read data"/>
             </when>
             <when value="FALSE">
-                <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
+                <param name="reads" argument="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
             </when>
         </conditional>
         <expand macro="trimmers"/>
@@ -104,19 +104,20 @@
     </inputs>
     <outputs>
         <collection name="paired_output" type="paired">
-            <data name="forward" format="fastqsanger.gz" from_work_dir="filt_forward.fastq.gz" />
-            <data name="reverse" format="fastqsanger.gz" from_work_dir="filt_reverse.fastq.gz" />
-            <filter>paired_cond['paired_select'] == 'TRUE'</filter>
+            <data name="forward" format="fastqsanger.gz" />
+            <data name="reverse" format="fastqsanger.gz" />
+            <filter>paired_cond['paired_select'] == "TRUE"</filter>
         </collection>
-        <data name="output" format="fastqsanger.gz" from_work_dir="filt_forward.fastq.gz">
-            <filter>paired_cond['paired_select'] == 'FALSE'</filter>
+        <data name="output" format="fastqsanger.gz" >
+            <filter>paired_cond['paired_select'] == "FALSE"</filter>
         </data>
         <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
             <filter>output_statistics</filter>
         </data>
     </outputs>
     <tests>
-        <!-- paired data -->
+        <!-- paired data 
+             currently removed `expect_num_outputs="2"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
         <test>
             <conditional name="paired_cond">
                 <param name="paired_select" value="TRUE"/>
@@ -127,21 +128,23 @@
                     </collection>
                 </param>
             </conditional>
-            <output_collection name="paired_output" count="2">
+            <output_collection name="paired_output" type="paired" count="2">
                 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
                 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
             </output_collection>
+            <output name="outtab" value="filterAndTrim_F3D0.tab" ftype="tabular"/>
         </test>
         <!-- single end data -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="paired_cond">
                 <param name="paired_select" value="FALSE"/>
                 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
             </conditional>
+            <param name="output_statistics" value="FALSE" />
             <output name="output" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
         </test>
         <!-- single end data trimming -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="paired_cond">
                 <param name="paired_select" value="FALSE"/>
                 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
@@ -150,10 +153,11 @@
             <param name="trim|trimLeft" value="150" />
             <param name="trim|trimRight" value="2" />
             <param name="trim|truncLen" value="2" />
+            <param name="output_statistics" value="FALSE" />
             <output name="output" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
         </test>
         <!-- single end data filtering -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="paired_cond">
                 <param name="paired_select" value="FALSE"/>
                 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
@@ -163,10 +167,12 @@
             <param name="filter|maxN" value="100" />
             <param name="filter|minQ" value="13" />
             <param name="filter|maxEE" value="1" />
+            <param name="output_statistics" value="FALSE" />
             <output name="output" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
         </test>
-        <!-- paired data w separate filters and trimmers for reverse -->
-        <test>
+        <!-- paired data w separate filters and trimmers for reverse 
+             currently removed `expect_num_outputs="1"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
+            <test>
             <conditional name="paired_cond">
                 <param name="paired_select" value="TRUE"/>
                 <param name="reads">
@@ -186,7 +192,8 @@
             <param name="seprev_cond|filter|maxN" value="100" />
             <param name="seprev_cond|filter|minQ" value="13" />
             <param name="seprev_cond|filter|maxEE" value="1" />
-            <output_collection name="paired_output" count="2"/>
+            <param name="output_statistics" value="FALSE" />
+            <output_collection name="paired_output" type="paired" count="2"/>
         </test>
     </tests>