--- a/unicycler.xml	Sat Sep 24 21:14:02 2022 +0000
+++ b/unicycler.xml	Fri Oct 21 16:02:46 2022 +0000
@@ -1,7 +1,8 @@
 <tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
+<description>pipeline for bacterial genomes</description>
     <macros>
         <token name="@TOOL_VERSION@">0.5.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">unicycler</xref>
@@ -18,44 +19,46 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 ## 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.is_of_type('fastqsanger')
+    #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
         #set fq1 = "fq1.fastq"
-    #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
+    #elif $paired_unpaired.fastq_input1.file_ext in $compressed
         #set fq1 = "fq1.fastq.gz"
     #end if
-    #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger')
+    #if $paired_unpaired.fastq_input2.file_ext in $uncompressed
         #set fq2 = "fq2.fastq"
-    #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz')
+    #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.is_of_type('fastqsanger')
+    #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed
         #set fq1 = "fq1.fastq"
-    #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz')
+    #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed
         #set fq1 = "fq1.fastq.gz"
     #end if
-    #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger')
+    #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed
         #set fq2 = "fq2.fastq"
-    #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz')
+    #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.is_of_type('fastqsanger')
+    #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
         #set fq = "fq.fastq"
-    #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
+    #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.is_of_type('fastqsanger')
+    #if $long.file_ext in $uncompressed
         #set lr = "lr.fastq"
-    #elif $long.is_of_type('fastqsanger.gz')
+    #elif $long.file_ext in $compressed
         #set lr = "lr.fastq.gz"
     #elif $long.is_of_type('fasta')
         #set lr = "lr.fasta"
@@ -138,22 +141,22 @@
                 <option value="none">None</option>
             </param>
             <when value="paired">
-                <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz"
+                <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
                     label="Select first set of reads" help="Specify dataset with forward reads"/>
-                <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz"
+                <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
                     label="Select second set of reads" help="Specify dataset with reverse reads"/>
             </when>
             <when value="paired_collection">
-                <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
+                <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
             </when>
             <when value="single">
-                <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz"
+                <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
                     label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
             </when>
             <when value="none">
             </when>
         </conditional>
-        <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/>
+        <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta,fastq,fastq.gz" label="Select long reads. If there are no long reads, leave this empty"/>
         <param argument="--mode" type="select" label="Select Bridging mode">
             <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
             <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>