--- a/dante_ltr_search.xml	Thu Aug 11 07:29:06 2022 +0000
+++ b/dante_ltr_search.xml	Mon Jan 30 10:05:47 2023 +0000
@@ -1,23 +1,19 @@
-<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.8.0" python_template_version="3.5">
+<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.2.2.0" python_template_version="3.5">
     <requirements>
-        <requirement type="package">blast</requirement>
-        <requirement type="package">r-optparse</requirement>
-        <requirement type="package">bioconductor-bsgenome</requirement>
-        <requirement type="package">bioconductor-biostrings</requirement>
-        <requirement type="package">bioconductor-rtracklayer</requirement>
-        <requirement type="package" version="3.7.12">python</requirement>
-
-    </requirements>
+        <requirement type="package">dante_ltr=0.2.2.0</requirement>
+     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python ${__tool_directory__}/detect_putative_ltr_wrapper.py --gff3 '$dante'
-          --reference_sequence '$reference' -M $max_missing --output output --cpu 32
+        echo \$PATH
+        &&
+        dante_ltr --gff3 '$dante'
+          --reference_sequence '$reference' -M $max_missing --output output --cpu \${GALAXY_SLOTS:-1}
         &&
         mv output.gff3 $te_ltr_gff
         &&
         mv output_statistics.csv $statistics
     ]]></command>
     <inputs>
-        <param type="data" name="dante" format="gff3" label="Filtered GFF3 output from DANTE pipeline"/>
+        <param type="data" name="dante" format="gff3" label="GFF3 output from DANTE pipeline - full output"/>
         <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" />
         <param type="integer" name="max_missing" min="0" max="3" value="1" label="Maximum number of missing protein domains to tolerate in full length retrotransposon" />
     </inputs>