--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clean_dante_ltr.xml	Tue Mar 08 13:24:33 2022 +0000
@@ -0,0 +1,34 @@
+<tool id="clean_dante_ltr" name="DANTE_LTR transposamble elements filtering" version="0.1.0" python_template_version="3.5">
+    <requirements>
+
+        <requirement type="package">r-optparse</requirement>
+        <requirement type="package">blast</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 ${__tool_directory__}/clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu 32
+        &&
+        mv output_clean.gff3 $dante_ltr_clean
+        &&
+        mv output_RM_lib.fasta $rm_lib
+    ]]></command>
+    <inputs>
+        <param type="data" name="dante_ltr" format="gff3" />
+        <param type="data" name="reference" format="fasta" />
+    </inputs>
+    <outputs>
+        <data name="dante_ltr_clean" format="gff3" label="Annotation of validated LTR transposable
+        elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
+        <data name="rm_lib" format="fasta" label="Non-redundant library of LTR transposable
+        elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
+    </outputs>
+    <help><![CDATA[
+        This tool takes output from DANTE_LTR search identifies good quality transposable elements.
+         Good quality TE are considered those which does not have any cross-similarity between distinct lineages.
+         Output from this tool is a annotation in GFF3 format and
+         non-redundant library of elements for custom RepeatMasker search.
+
+    ]]></help>
+</tool>
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