--- a/unicycler.xml	Tue Dec 19 15:58:30 2023 +0000
+++ b/unicycler.xml	Sun Jul 07 19:46:39 2024 +0000
@@ -2,7 +2,7 @@
 <description>pipeline for bacterial genomes</description>
     <macros>
         <token name="@TOOL_VERSION@">0.5.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <edam_topics>
         <edam_topic>topic_0196</edam_topic>
@@ -23,48 +23,46 @@
 #end for
 
 ## Preparing files
-#set $uncompressed = ('fastqsanger','fastq')
-#set $compressed = ('fastqsanger.gz','fastq.gz')
 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
-    #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
+    #if $paired_unpaired.fastq_input1.is_of_type("fastq.gz"):
+        #set fq1 = "fq1.fastq.gz"
+    #else
         #set fq1 = "fq1.fastq"
-    #elif $paired_unpaired.fastq_input1.file_ext in $compressed
-        #set fq1 = "fq1.fastq.gz"
     #end if
-    #if $paired_unpaired.fastq_input2.file_ext in $uncompressed
+    #if $paired_unpaired.fastq_input2.is_of_type("fastq.gz"):
+        #set fq2 = "fq2.fastq.gz"
+    #else
         #set fq2 = "fq2.fastq"
-    #elif $paired_unpaired.fastq_input2.file_ext in $compressed
-        #set fq2 = "fq2.fastq.gz"
     #end if
     ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
     ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
-    #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed
+    #if $paired_unpaired.fastq_input1.forward.is_of_type("fastq.gz"):
+        #set fq1 = "fq1.fastq.gz"
+    #else
         #set fq1 = "fq1.fastq"
-    #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed
-        #set fq1 = "fq1.fastq.gz"
     #end if
-    #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed
+    #if $paired_unpaired.fastq_input1.reverse.is_of_type("fastq.gz"):
+        #set fq2 = "fq2.fastq.gz"
+    #else
         #set fq2 = "fq2.fastq"
-    #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed
-        #set fq2 = "fq2.fastq.gz"
     #end if
     ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
     ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
-    #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
+    #if $paired_unpaired.fastq_input1.is_of_type("fastqsanger.gz"):
+        #set fq = "fq.fastq.gz"
+    #else
         #set fq = "fq.fastq"
-    #elif $paired_unpaired.fastq_input1.file_ext in $compressed
-        #set fq = "fq.fastq.gz"
     #end if
     ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
 #end if
 #if $long
-    #if $long.file_ext in $uncompressed
+    #if $long.is_of_type("fastq"):
         #set lr = "lr.fastq"
-    #elif $long.file_ext in $compressed
+    #elif $long.is_of_type("fastq.gz"):
         #set lr = "lr.fastq.gz"
-    #elif $long.is_of_type('fasta')
+    #elif $long.is_of_type("fasta")
         #set lr = "lr.fasta"
     #end if
     ln -s '${long}' '$lr' &&