--- a/dante_gff_to_dna.xml	Fri Apr 03 07:27:59 2020 -0400
+++ b/dante_gff_to_dna.xml	Wed Jan 25 13:06:55 2023 +0000
@@ -1,20 +1,18 @@
-<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.0.0">
+<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.1.4">
   <description> Tool to extract nucleotide sequences of protein domains found by DANTE </description>
   <requirements>
-    <requirement type="package">biopython</requirement>
-    <requirement type="package" version="1.0">rexdb</requirement>
-    <requirement type="set_environment">REXDB</requirement>
+    <requirement type="package">dante=0.1.4</requirement>
   </requirements>
   <command>
     TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp;
-    python3 ${__tool_directory__}/dante_gff_to_dna.py --domains_gff ${domains_gff} --input_dna ${input_dna} --out_dir \$TEMP_DIR_LINEAGES
+    /mnt/raid/users/petr/workspace/dante/dante_gff_to_dna.py --domains_gff ${domains_gff} --input_dna ${input_dna} --out_dir \$TEMP_DIR_LINEAGES
 
     #if $extend_edges:
 	  --extended True
     #else:
 	  --extended False
     #end if
-	  --classification \${REXDB}/${db_type}_class
+	  --database ${database}
     &amp;&amp;
 
     cat \$TEMP_DIR_LINEAGES/*fasta > $out_fasta &amp;&amp;
@@ -23,12 +21,12 @@
   <inputs>
 	  <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="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>
+	  <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="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"/>
   </inputs>