# HG changeset patch
# User petr-novak
# Date 1759919155 0
# Node ID a9d7ebf988f91fa202f44fd1f1786aa23a361d5e
# Parent  5210db15a5facdbee39c9c7c39552f4e6fb400a0
planemo upload commit e69c5698ba012f5ddd884d4050f818b4450f5874-dirty

diff -r 5210db15a5fa -r a9d7ebf988f9 dante.xml
--- a/dante.xml	Thu Jun 19 10:21:26 2025 +0000
+++ b/dante.xml	Wed Oct 08 10:25:55 2025 +0000
@@ -1,7 +1,7 @@
-<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="2.9.1">
+<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="2.10.1">
   <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description>
   <requirements>
-    <requirement type="package" version="0.2.9">dante</requirement>
+    <requirement type="package" version="0.2.10">dante</requirement>
   </requirements>
   <stdio>
     <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
@@ -15,23 +15,12 @@
     #else
       INPUT_SEQUENCES=$(input_sequences)
     #end if
-    &&
-    grep -c "^>" \${INPUT_SEQUENCES}
-    &&
-    NUMBER_OF_SEQUENCES=`grep -c "^>" \${INPUT_SEQUENCES}`
-    &&
-    if [ \${NUMBER_OF_SEQUENCES} -gt 10000 ]; then
-      SHORT_READS="--short_reads";
-    else
-      SHORT_READS="";
-    fi
 
     &&
     dante --query \${INPUT_SEQUENCES} --domain_gff ${DomGff}
 	  --database $database
       --scoring_matrix ${scoring_matrix}
       --cpu \${GALAXY_SLOTS:-1}
-      \${SHORT_READS}
 
     &&
     dante_gff_output_filtering.py --dom_gff ${DomGff}
diff -r 5210db15a5fa -r a9d7ebf988f9 dante_gff_output_filtering.xml
--- a/dante_gff_output_filtering.xml	Thu Jun 19 10:21:26 2025 +0000
+++ b/dante_gff_output_filtering.xml	Wed Oct 08 10:25:55 2025 +0000
@@ -1,7 +1,7 @@
-<tool id="domains_filter" name="Protein Domains Filter" version="2.9.1">
+<tool id="domains_filter" name="Protein Domains Filter" version="2.10.1">
   <description> Tool for filtering of gff3 output from DANTE. Filtering can be performed based domain type and alignment quality. </description>
     <requirements>
-        <requirement type="package" version="0.2.9">dante</requirement>
+        <requirement type="package" version="0.2.10">dante</requirement>
     </requirements>
     <stdio>
         <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
diff -r 5210db15a5fa -r a9d7ebf988f9 dante_gff_to_dna.xml
--- a/dante_gff_to_dna.xml	Thu Jun 19 10:21:26 2025 +0000
+++ b/dante_gff_to_dna.xml	Wed Oct 08 10:25:55 2025 +0000
@@ -1,16 +1,14 @@
-<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="2.9.1">
+<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="2.10.1">
   <description> Tool to extract nucleotide sequences of protein domains found by DANTE </description>
   <requirements>
-    <requirement type="package" version="0.2.9">dante</requirement>
+    <requirement type="package" version="0.2.10">dante</requirement>
   </requirements>
   <command>
     TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp;
     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
+	  --extended
     #end if
 	  --database ${database}
     &amp;&amp;
diff -r 5210db15a5fa -r a9d7ebf988f9 dante_gff_to_tabular.xml
--- a/dante_gff_to_tabular.xml	Thu Jun 19 10:21:26 2025 +0000
+++ b/dante_gff_to_tabular.xml	Wed Oct 08 10:25:55 2025 +0000
@@ -1,6 +1,6 @@
-<tool id="gff_to_tabular" name="Convert dante gff3 to tab delimited file" version="2.9.1" python_template_version="3.5">
+<tool id="gff_to_tabular" name="Convert dante gff3 to tab delimited file" version="2.10.1" python_template_version="3.5">
     <requirements>
-        <requirement type="package" version="0.2.9">dante</requirement>
+        <requirement type="package" version="0.2.10">dante</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         summarize_gff.R '$inputgff' '$output'
diff -r 5210db15a5fa -r a9d7ebf988f9 summarize_gff.xml
--- a/summarize_gff.xml	Thu Jun 19 10:21:26 2025 +0000
+++ b/summarize_gff.xml	Wed Oct 08 10:25:55 2025 +0000
@@ -19,5 +19,4 @@
     <help><![CDATA[
         TODO: Fill in help.
     ]]></help>
-</tool>
-z
\ No newline at end of file
+</tool>
\ No newline at end of file