--- a/prinseq.xml	Fri Mar 03 14:58:49 2017 -0500
+++ b/prinseq.xml	Mon May 15 11:03:57 2017 -0400
@@ -617,36 +617,36 @@
     </inputs>
 
     <outputs>
-        <data format="fastq" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq"
+        <data format_source="input_singles" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq"
             label="${tool.name} on ${on_string}: Good sequences" >
             <filter>seq_type['seq_type_opt'] == "single"</filter>
         </data>
-        <data format="fastq" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq"
+        <data format_source="input_singles" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences" >
             <filter>seq_type['seq_type_opt'] == "single"</filter>
         </data>
 
-        <data format="fastq" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq"
+        <data format_source="input_mate1" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq"
             label="${tool.name} on ${on_string}: Good sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq"
+        <data format_source="input_mate1" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq"
             label="${tool.name} on ${on_string}: Good singleton sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq"
+        <data format_source="input_mate1" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq"
+        <data format_source="input_mate2" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq"
             label="${tool.name} on ${on_string}: Good sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq"
+        <data format_source="input_mate2" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq"
             label="${tool.name} on ${on_string}: Good singleton sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format="fastq" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"
+        <data format_source="input_mate2" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
@@ -658,7 +658,7 @@
     <tests>
         <test>
             <param name='seq_type_opt' value="single"/>
-            <param name="input_singles" value="prinseq_input_sequences.fastq"/>
+            <param name="input_singles" value="prinseq_input_sequences.fastq" ftype="fastqsanger"/>
             <param name='apply_filter_treatments' value="true"/>
             <param name='apply_length_filter_treatments' value="true"/>
             <param name='apply_min_length_filter_treatments' value="true"/>
@@ -691,7 +691,7 @@
             <param name="window_quality_trimming_treatments" value="1"/>
             <param name="step_quality_trimming_treatments" value="1"/>
 
-            <output name="good_sequence_file" file="prinseq_good_sequences.fastq"/>
+            <output name="good_sequence_file" file="prinseq_good_sequences.fastq" ftype="fastqsanger"/>
         </test>
     </tests>