--- a/flye.xml	Tue Sep 25 05:24:27 2018 -0400
+++ b/flye.xml	Fri Sep 28 19:18:54 2018 -0400
@@ -9,7 +9,17 @@
     <![CDATA[
 
     #for $counter, $input in enumerate($inputs):
-        ln -s '$input' ./input_${counter}.${input.ext} &&
+
+        #if $input.is_of_type('fastqsanger', 'fastq'):
+            #set $ext = 'fastq'
+        #elif $input.is_of_type('fastqsanger.gz'):
+            #set $ext = 'fastq.gz'
+        #elif $input.is_of_type('fasta.gz'):        
+            #set $ext = 'fasta.gz'
+        #elif $input.is_of_type('fasta'):        
+            #set $ext = 'fasta'
+        #end if
+        ln -s '$input' ./input_${counter}.${ext} &&
     #end for
     
     flye
@@ -28,7 +38,7 @@
     2>&1
     ]]></command>
     <inputs>
-        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input reads" />
+        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
         <param name="mode" type="select" label="Mode">
             <option value="--nano-raw">Nanopore raw</option>
             <option value="--nano-corr">Nanopore corrected</option>