--- a/breseq.xml	Mon Dec 02 04:51:27 2019 -0500
+++ b/breseq.xml	Wed Apr 07 12:17:45 2021 +0000
@@ -7,7 +7,7 @@
     </macros>
 
     <requirements>
-        <requirement type="package" version="0.34.0">breseq</requirement>
+        <requirement type="package" version="0.35.5">breseq</requirement>
         <requirement type="package" version="1.32">tar</requirement>
     </requirements>
 
@@ -130,7 +130,7 @@
             </param>
             <when value="detect">
 
-                <param name="fastqs" type="data" format="fastq" multiple="true" label="Fastq Read Files" />
+                <param name="fastqs" type="data" format="fastq,fastq.gz" multiple="true" label="Fastq Read Files" />
 
                 <param argument="--polymorphism-prediction" name="polymorphism_prediction" type="select" label="Detection Mode" help="**Polymorphism mode**: Detect variants with frequencies between 0% and 100% if a mixture model is well-supported by the read alignment evidence. Use to analyze a mixed population of genomes evolved from a common ancestor. **Consensus mode**: Detect variants present in 100% of the sample. Use when re-sequencing a clonal haploid genome. This mode is the default.">
                     <option value="" selected="true">Consensus</option>
@@ -216,7 +216,7 @@
             </repeat>
             <conditional name="run">
                 <param name="mode" value="detect" />
-                <param name="fastqs" value="lambda.short_sequence_repeats.fastq" />
+                <param name="fastqs" value="lambda.short_sequence_repeats.fastq.gz" ftype="fastq.gz" />
                 <param name="polymorphism_prediction" value="" />
                 <param name="name" value="smallest" />
                 <param name="predict_junctions" value="" />
@@ -247,7 +247,7 @@
             </repeat>
             <conditional name="run">
                 <param name="mode" value="detect" />
-                <param name="fastqs" value="lambda.short_sequence_repeats.fastq" />
+                <param name="fastqs" value="lambda.short_sequence_repeats.fastq.gz" ftype="fastq.gz"/>
                 <param name="polymorphism_prediction" value="" />
                 <param name="name" value="smallest" />
                 <param name="predict_junctions" value="" />