--- a/arriba.xml	Wed Oct 13 18:45:16 2021 +0000
+++ b/arriba.xml	Fri Feb 11 19:04:06 2022 +0000
@@ -161,6 +161,12 @@
     #if $options.max_itd_length
         -l $options.max_itd_length
     #end if
+    #if $options.min_itd_allele_fraction
+        -z $options.min_itd_allele_fraction
+    #end if
+    #if $options.min_itd_supporting_reads
+        -Z $options.min_itd_supporting_reads
+    #end if
     $options.duplicate_marking
     $options.fill_discarded_columns
     $options.fill_the_gaps
@@ -381,7 +387,7 @@
             <param name="covered_fraction" argument="-C" type="float" value="" min="0." max="1.0" optional="true" label="Covered fraction">
                 <help>Ignore virally associated events if the virus is not fully expressed, 
                       i.e., less than the given fraction of the viral contig is transcribed.
-                      Default: 0.150000
+                      Default: 0.050000
                 </help>
             </param>
             <param name="max_itd_length" argument="-l" type="integer" value="" min="1" optional="true" label="Maximum length of internal tandem duplications">
@@ -389,6 +395,14 @@
                       Default: 100
                 </help>
             </param>
+            <param name="min_itd_allele_fraction" argument="-z" type="float" value="" min="0." max="1.0" optional="true" label="Required fraction of supporting reads to report an internal tandem duplication">
+                <help> Default: 0.070000 
+                </help>
+            </param>
+            <param name="min_itd_supporting_reads" argument="-Z" type="integer" value="" min="1" optional="true" label="Required number of supporting reads to report an internal tandem duplication">
+                <help> Default: 10
+                </help>
+            </param>
             <param name="duplicate_marking" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Use aligners duplicate marking">
                 <help>Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a
                       preceding program using the BAM_FDUP flag. This makes sense when unique molecular
@@ -442,8 +456,8 @@
             </conditional>
             <conditional name="genome">
                 <param name="genome_source" value="history"/>
-                <param name="assembly" ftype="fasta" value="genome.fasta"/>
-                <param name="annotation" ftype="gtf" value="genome.gtf"/>
+                <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
+                <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
             </conditional>
             <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
             <conditional name="visualization">
@@ -465,8 +479,8 @@
             </conditional>
             <conditional name="genome">
                 <param name="genome_source" value="history"/>
-                <param name="assembly" ftype="fasta" value="genome.fasta"/>
-                <param name="annotation" ftype="gtf" value="genome.gtf"/>
+                <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
+                <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
             </conditional>
             <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
             <conditional name="visualization">