--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dante_ltr_search.xml	Tue Mar 08 13:24:33 2022 +0000
@@ -0,0 +1,40 @@
+<tool id="dante_ltr_search" name="DANTE_LTR transposable element identification" version="0.1.0" 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">biocondutor-biostrings</requirement>
+        <requirement type="package">bioconductor-rtracklayer</requirement>
+
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript ${__tool_directory__}/extract_putative_ltr.R --gff3 '$dante' --reference_sequence '$reference' --output output --cpu 32
+        &&
+        mv output.gff3 $te_ltr_gff
+    ]]></command>
+    <inputs>
+        <param type="data" name="dante" format="gff3" label="Filtered gff3 output from DANTE pipeline"/>
+        <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" />
+    </inputs>
+    <outputs>
+        <data name="te_ltr_gff" format="gff3" label="Annotation of detected LTR transposable elements
+         based on the annotation $dante.hid and reference $reference.hid" />
+    </outputs>
+    <help><![CDATA[
+        This tool uses output from DANTE annotation pipeline to identify full length LTR
+        transposable elements. Output is in the GFF3 format and include annotation of
+        5' and 3' Longe Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS).
+
+        All identified elements contains complete set of protein domains as defined in
+        REXdb_. Based on the results detection  structural feature,
+        elements falls into four categories:
+
+        - elements with domains, 5'LTR, 3'LTR, TSD and PBS
+        - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found)
+        - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found)
+        - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found)
+
+       .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1
+
+    ]]></help>
+</tool>
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