--- a/dante.xml	Fri Apr 03 07:27:59 2020 -0400
+++ b/dante.xml	Wed Jan 25 13:06:55 2023 +0000
@@ -1,10 +1,7 @@
-<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.0">
+<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.4">
   <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description>
   <requirements>
-    <requirement type="package">last</requirement>
-    <requirement type="package">numpy</requirement>
-    <requirement type="package" version="1.0">rexdb</requirement>
-    <requirement type="set_environment">REXDB</requirement>
+    <requirement type="package">dante=0.1.4</requirement>
   </requirements>
   <stdio>
     <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
@@ -12,7 +9,7 @@
   </stdio>
   <command>
     #if str($input_type.input_type_selector) == "aln"
-      python3 ${__tool_directory__}/parse_aln.py -a $(input_sequences) -f sequences.fasta -p sequences.profile
+      parse_aln.py -a $(input_sequences) -f sequences.fasta -p sequences.profile
       &amp;&amp;
       INPUT_SEQUENCES="sequences.fasta"
     #else    
@@ -21,13 +18,12 @@
     &amp;&amp;
 
 
-    python3 ${__tool_directory__}/dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff}
-	  --protein_database \${REXDB}/${db_type}_pdb
-	  --classification \${REXDB}/${db_type}_class
-    --scoring_matrix ${scoring_matrix}
+    dante --query \${INPUT_SEQUENCES} --domain_gff ${DomGff}
+	  --database $database
+      --scoring_matrix ${scoring_matrix}
 
     &amp;&amp;
-    python3 ${__tool_directory__}/dante_gff_output_filtering.py --dom_gff ${DomGff}
+    dante_gff_output_filtering.py --dom_gff ${DomGff}
     --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered}
     --output_dir .
     --selected_dom All --th_identity 0.35
@@ -37,12 +33,12 @@
 
     #if str($input_type.input_type_selector) == "aln"
      &amp;&amp;
-     python3 ${__tool_directory__}/coverage2gff.py -p sequences.profile -g ${DomGff}
+     coverage2gff.py -p sequences.profile -g ${DomGff}
     #end if
 
     #if str($iterative) == "Yes"
     &amp;&amp;
-    python3 ${__tool_directory__}/dante_gff_output_filtering.py --dom_gff ${DomGff}
+   dante_gff_output_filtering.py --dom_gff ${DomGff}
     --domains_prot_seq domains_filtered.fasta --domains_filtered domains_filtered.gff
     --output_dir .
     --selected_dom All --th_identity 0.35
@@ -53,22 +49,22 @@
 
 
 
-    python3 ${__tool_directory__}/fasta2database.py domains_filtered.fasta domains_filtered.db
+    fasta2database.py domains_filtered.fasta domains_filtered.db
     domains_filtered.class
     &amp;&amp;
 
     lastdb -p domains_filtered.db domains_filtered.db
     &amp;&amp;
 
-    python3 ${__tool_directory__}/dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff2}
+    dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff2}
 	  --protein_database domains_filtered.db
 	  --classification domains_filtered.class
-    --scoring_matrix BL80
+      --scoring_matrix BL80
 
 
     #if str($input_type.input_type_selector) == "aln"
      &amp;&amp;
-     python3 ${__tool_directory__}/coverage2gff.py -p sequences.profile -g ${DomGff2}
+     coverage2gff.py -p sequences.profile -g ${DomGff2}
     #end if
     #end if
 
@@ -87,13 +83,12 @@
         <param name="input_sequences" type="data" format="txt" label="Sequences in ALN format (extracted from RepeatExplorer)"/>
       </when>
     </conditional>
-    <param name="db_type" type="select" label="Select taxon and protein domain database version (REXdb)" help="">
-      <options from_file="rexdb_versions.loc">
-        <column name="name" index="0"/>
-        <column name="value" index="1"/>
-      </options>
+    <param name="database" type="select" label="Select REXdb database">
+        <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>
     </param>
-
     <param name="scoring_matrix" type="select" label="Select scoring matrix">
       <option value="BL80" selected="true" >BLOSUM80</option>
       <option value="BL62">BLOSUM62</option>