--- a/filtlong.xml	Mon Sep 17 16:16:07 2018 -0400
+++ b/filtlong.xml	Wed Sep 19 08:21:21 2018 -0400
@@ -43,7 +43,7 @@
     '$input_file' > output.fastq
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="fastq" label="Input FASTQ" help="FASTQ of input reads"/>
+        <param name="input_file" type="data" format="fastqsanger" label="Input FASTQ" help="FASTQ of input reads"/>
         <section name="output_thresholds" title="Output thresholds">
             <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/>
             <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
@@ -53,8 +53,8 @@
         </section>
         <section name="external_references" title="External references">
             <param argument="--assembly" type="data" format="fasta" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
-            <param argument="--illumina_1" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
-            <param argument="--illumina_2" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
+            <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
+            <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
         </section>
         <section name="score_weights" title="Score weights">
             <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
@@ -70,26 +70,26 @@
         </section>
     </inputs>
     <outputs>
-        <data name="outfile" format="fastq" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
+        <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_file" ftype="fastq" value="test.fastq"/>
+            <param name="input_file" ftype="fastqsanger" value="test.fastq"/>
             <param name="min_length" value="1000"/>
             <param name="keep_percent" value="50"/>
             <param name="target_bases" value="500000000"/>
-            <output name="outfile" ftype="fastq" file="output.fastq"/>
+            <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
         </test>
         <test>
-            <param name="input_file" ftype="fastq" value="test_reference.fasta"/>
-            <param name="illumina_1" ftype="fastq.gz" value="test_reference_1.fastq.gz"/>
-            <param name="illumina_2" ftype="fastq.gz" value="test_reference_2.fastq.gz"/>
+            <param name="input_file" ftype="fastqsanger" value="test_reference.fasta"/>
+            <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
+            <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
             <param name="min_length" value="1000"/>
             <param name="keep_percent" value="90"/>
             <param name="target_bases" value="500000000"/>
             <param name="trim" value="True"/>
             <param name="split" value="500"/>
-            <output name="outfile" ftype="fastq" file="output_reference.fastq"/>
+            <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
         </test>
     </tests>
     <help><![CDATA[