--- a/porechop.xml	Wed Sep 06 12:29:17 2017 -0400
+++ b/porechop.xml	Sat Oct 14 10:52:30 2017 -0400
@@ -27,6 +27,8 @@
 
         --input ${input}
 
+        --format ${out_format}
+
         #if str($demux_section.demux_options.demux) == "yes":
             --barcode_dir out
         #else:
@@ -85,6 +87,11 @@
 
         <param argument="--input" type="data" format="fastq,fasta" label="Input reads" />
 
+        <param name="out_format" type="select" label="Output format">
+            <option value="fastq" selected="true">fastq</option>
+            <option value="fasta">fasta</option>
+        </param>
+
         <section name="demux_section" title="Demultiplexing Options" expanded="True">
             <conditional name="demux_options">
             <param name="demux" type="select" label="Perform demultiplexing" help="">
@@ -136,6 +143,16 @@
             <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fastqsanger" />
         </collection>
 
+
+        <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}">
+            <filter>out_format == 'fastq'</filter>
+            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fastqsanger" />
+        </collection>
+        <collection type="list" name="output_collection_fasta" label="${tool.name} on ${on_string}">
+            <filter>out_format == 'fasta'</filter>
+            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fasta" />
+        </collection>
+
     </outputs>
 
     <!-- ***************************************************************** -->
@@ -144,7 +161,7 @@
         <test>
             <param name="input" value="test_barcodes.fastq" ftype="fastq" />
             <param name="demux" value="yes" />
-            <output_collection name="output" type="list">
+            <output_collection name="output_collection_fastq" type="list">
                 <element name="BC01.fastq" file="bar1/BC01.fastq" compare="diff" decompress="true"/>
                 <element name="BC02.fastq" file="bar1/BC02.fastq" compare="diff" decompress="true"/>
                 <element name="BC03.fastq" file="bar1/BC03.fastq" compare="diff" decompress="true"/>
@@ -155,7 +172,7 @@
             <param name="input" value="test_barcodes.fastq" ftype="fastq" />
             <param name="demux" value="yes" />
             <param name="require_two_barcodes" value="True" />
-            <output_collection name="output" type="list">
+            <output_collection name="output_collection_fastq" type="list">
                 <element name="BC01.fastq" file="bar2/BC01.fastq" compare="diff" decompress="true"/>
                 <element name="BC02.fastq" file="bar2/BC02.fastq" compare="diff" decompress="true"/>
                 <element name="BC03.fastq" file="bar2/BC03.fastq" compare="diff" decompress="true"/>
@@ -166,7 +183,7 @@
             <param name="input" value="test_barcodes.fastq" ftype="fastq" />
             <param name="demux" value="yes" />
             <param name="trim" value="yes" />
-            <output_collection name="output" type="list">
+            <output_collection name="output_collection_fastq" type="list">
                 <element name="BC01.fastq" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>
                 <element name="BC02.fastq" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>
                 <element name="BC03.fastq" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>