diff --git a/tools/rna_tools/ribotaper/macros.xml b/tools/rna_tools/ribotaper/macros.xml
index 4ac71c28ad..2e00e4be53 100644
--- a/tools/rna_tools/ribotaper/macros.xml
+++ b/tools/rna_tools/ribotaper/macros.xml
@@ -1,11 +1,11 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3.1a</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">1.3.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">ribotaper</requirement>
-            <requirement type="package" version="9.1">coreutils</requirement>
-            <requirement type="package" version="9.54.0">ghostscript</requirement>
+            <requirement type="package" version="9.5">coreutils</requirement>
+            <requirement type="package" version="10.07.0">ghostscript</requirement>
 
         </requirements>
     </xml>
diff --git a/tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml b/tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml
index d39ba3bbf1..4009889695 100644
--- a/tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml
+++ b/tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml
@@ -26,7 +26,7 @@
 
     ]]></command>
     <inputs>
-        <param name="gtf" type="data" format="GTF" label="Annotation file"
+        <param name="gtf" type="data" format="gtf" label="Annotation file"
             help="The GTF file should contain: 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row."/>
         <conditional name="reference_genome">
             <param name="source" type="select" label="Source for the genome" help="Built-in references were created using default options.">
diff --git a/tools/rna_tools/ribotaper/ribotaper_part3_main.xml b/tools/rna_tools/ribotaper/ribotaper_part3_main.xml
index 0404c93a00..d37285c24b 100644
--- a/tools/rna_tools/ribotaper/ribotaper_part3_main.xml
+++ b/tools/rna_tools/ribotaper/ribotaper_part3_main.xml
@@ -8,8 +8,8 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        #if $annotation_path.is_of_type("tgz")
-            tar -xzvf '${annotation_path}' &&
+        #if $annotation_path.is_of_type("tar.gz")
+            tar -xvzf '${annotation_path}' &&
         #else
              tar -xvf '${annotation_path}' &&
         #end if
@@ -22,9 +22,9 @@
             \${GALAXY_SLOTS:-12}
     ]]></command>
     <inputs>
-        <param name="annotation_path" type="data" format="tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
-        <param name="ribo_bam" type="data" format="BAM" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
-        <param name="rna_bam" type="data" format="BAM" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
+        <param name="annotation_path" type="data" format="tar.gz,tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
+        <param name="ribo_bam" type="data" format="bam" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
+        <param name="rna_bam" type="data" format="bam" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
         <param name="read_lenghts_ribo" type="text" value="26,28,29"  label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29.
             Please run 'ribotaper part 2' to deterimine appropriate values.">
             <sanitizer invalid_char="">
@@ -55,6 +55,12 @@
         <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="${tool.name} on ${on_string}: ORF categories (length/coverage)"/>
     </outputs>
     <tests>
+        <test expect_num_outputs="8">
+            <param name="annotation_path" value="annotation_path.tgz" ftype="tar.gz"/>
+            <param name="ribo_bam" value="test_ribo.bam"/>
+            <param name="rna_bam" value="test_rna.bam"/>
+            <output name="output2" file="ORFs_genes_found"/>
+        </test>
         <test expect_num_outputs="8">
             <param name="annotation_path" value="annotation_path.tgz"/>
             <param name="ribo_bam" value="test_ribo.bam"/>