# HG changeset patch
# User petr-novak
# Date 1730819675 0
# Node ID f0663cdbae664f5bff0d089704b7cadd6a514cf8
# Parent  8f2bd3cae2de6979dc102a8fc397c2fcc043da60
planemo upload commit 29868d121127a8bb509a42fb917b09f669ad4a09-dirty

diff -r 8f2bd3cae2de -r f0663cdbae66 dante.xml
--- a/dante.xml	Wed Jun 21 08:50:27 2023 +0000
+++ b/dante.xml	Tue Nov 05 15:14:35 2024 +0000
@@ -1,7 +1,7 @@
-<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.8">
+<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="2.5.1">
   <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description>
   <requirements>
-    <requirement type="package">dante=0.1.8</requirement>
+    <requirement type="package">dante=0.2.5</requirement>
   </requirements>
   <stdio>
     <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
@@ -83,10 +83,11 @@
       </when>
     </conditional>
     <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="scoring_matrix" type="select" label="Select scoring matrix">
       <option value="BL80" selected="true" >BLOSUM80</option>
diff -r 8f2bd3cae2de -r f0663cdbae66 dante_gff_output_filtering.xml
--- a/dante_gff_output_filtering.xml	Wed Jun 21 08:50:27 2023 +0000
+++ b/dante_gff_output_filtering.xml	Tue Nov 05 15:14:35 2024 +0000
@@ -1,7 +1,7 @@
-<tool id="domains_filter" name="Protein Domains Filter" version="1.1.8">
+<tool id="domains_filter" name="Protein Domains Filter" version="2.5.1">
   <description> Tool for filtering of gff3 output from DANTE. Filtering can be performed based domain type and alignment quality. </description>
     <requirements>
-        <requirement type="package">dante=0.1.8</requirement>
+        <requirement type="package">dante=0.2.5</requirement>
     </requirements>
     <stdio>
         <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
diff -r 8f2bd3cae2de -r f0663cdbae66 dante_gff_to_dna.xml
--- 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"/>
diff -r 8f2bd3cae2de -r f0663cdbae66 dante_gff_to_tabular.xml
--- a/dante_gff_to_tabular.xml	Wed Jun 21 08:50:27 2023 +0000
+++ b/dante_gff_to_tabular.xml	Tue Nov 05 15:14:35 2024 +0000
@@ -1,6 +1,6 @@
-<tool id="gff_to_tabular" name="Convert dante gff3 to tab delimited file" version="1.1.8" python_template_version="3.5">
+<tool id="gff_to_tabular" name="Convert dante gff3 to tab delimited file" version="2.5.1" python_template_version="3.5">
     <requirements>
-        <requirement type="package">dante=0.1.8</requirement>
+        <requirement type="package">dante=0.2.5</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         summarize_gff.R '$inputgff' '$output'
diff -r 8f2bd3cae2de -r f0663cdbae66 summarize_gff.xml
--- a/summarize_gff.xml	Wed Jun 21 08:50:27 2023 +0000
+++ b/summarize_gff.xml	Tue Nov 05 15:14:35 2024 +0000
@@ -1,6 +1,6 @@
-<tool id="gff_summary" name="Summarize gff3 output from DANTE" version="1.1.8" python_template_version="3.5">
+<tool id="gff_summary" name="Summarize gff3 output from DANTE" version="2.5.1" python_template_version="3.5">
     <requirements>
-        <requirement type="package">dante=0.1.8</requirement>
+        <requirement type="package">dante=0.2.5</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         summarize_gff.R '$inputgff' '$output' '$group'