--- a/commet.xml	Mon Aug 17 10:38:36 2020 -0400
+++ b/commet.xml	Thu May 06 12:45:20 2021 +0000
@@ -1,5 +1,4 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="commet" name="Commet" version="24.7.14">
+<tool id="commet" name="Commet" version="24.7.14+galaxy0" profile="@PROFILE@">
     <description>COmpare Multiple METagenomes</description>
     <macros>
         <import>macros.xml</import>
@@ -7,8 +6,8 @@
     <requirements>
         <requirement type="package" version="24.7.14">commet</requirement>
     </requirements>
-    <command><![CDATA[
-        #for $i, $set in enumerate( $sets )
+    <command detect_errors="exit_code"><![CDATA[
+        #for $i, $set in enumerate($sets):
             echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt &&
         #end for
         Commet.py
@@ -16,18 +15,15 @@
         -t ${t}
         -l ${l}
         -e ${e}
-        #if str( $options_advanced.options_advanced_selector ) == "advanced"
+        #if str($options_advanced.options_advanced_selector) == "advanced":
             -m ${options_advanced.m}
             -n ${options_advanced.n}
         #end if
         commet_input_sets.txt
-
     ]]></command>
-
     <inputs>
-        <!-- Input data files -->
         <repeat name="sets" title="Read sets" min="1">
-            <param name="reads" type="data" multiple="true" format="fasta, fastq" label="Dataset" help="Accept fasta/fastq"/>
+            <param name="reads" type="data" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" label="Dataset" help="Accept fasta/fastq"/>
         </repeat>
         <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
         <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
@@ -73,13 +69,13 @@
         <test>
             <param name="input_type" value="list" />
             <repeat name="sets">
-                <param name="reads" value="commet/A.fa" ftype="fasta" />
+                <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" />
             </repeat>
             <repeat name="sets">
-                <param name="reads" value="commet/B.fa,commet/C.fa" ftype="fasta" />
+                <param name="reads" value="commet/B.fa.gz,commet/C.fa.gz" ftype="fasta.gz" />
             </repeat>
             <repeat name="sets">
-                <param name="reads" value="commet/D.fa" ftype="fasta" />
+                <param name="reads" value="commet/D.fa.gz" ftype="fasta.gz" />
             </repeat>
             <param name="plain_outputs" value="True"/>
             <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>