--- a/dante_gff_to_dna.xml	Wed Jun 21 08:50:27 2023 +0000
+++ b/dante_gff_to_dna.xml	Tue Nov 05 15:14:35 2024 +0000
@@ -1,7 +1,7 @@
-<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.1.8">
+<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="2.5.1">
   <description> Tool to extract nucleotide sequences of protein domains found by DANTE </description>
   <requirements>
-    <requirement type="package">dante=0.1.8</requirement>
+    <requirement type="package">dante=0.2.5</requirement>
   </requirements>
   <command>
     TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp;
@@ -22,10 +22,11 @@
 	  <param format="fasta" type="data" name="input_dna" label="Input DNA" help="Choose input DNA sequence(s) to extract the domains from" />
 	  <param format="gff" type="data" name="domains_gff" label="Protein domains GFF" help="Choose filtered protein domains GFF3 (DANTE's output)" />
 	  <param name="database" type="select" label="Select REXdb database">
+        <option value="Viridiplantae_v4.0" selected="true">Viridiplantae_v4.0</option>
         <option value="Viridiplantae_v3.0" selected="true">Viridiplantae_v3.0</option>
         <option value="Metazoa_v3.1" selected="true">Metazoa_v3.1</option>
         <option value="Viridiplantae_v2.2" selected="true">Viridiplantae_v2.2</option>
-        <option value="Metazoa_v3.0" selected="true">Metazoa_v3.1</option>
+        <option value="Metazoa_v3.0" selected="true">Metazoa_v3.0</option>
       </param>
 
 	  <param name="extend_edges" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Extend sequence edges" help="Extend extracted sequence edges to the full length of database domains sequences"/>