diff clean_dante_ltr.xml @ 3:6ae4a341d1f3 draft

"planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"

--- a/clean_dante_ltr.xml	Tue Apr 12 12:55:32 2022 +0000
+++ b/clean_dante_ltr.xml	Tue May 03 12:38:12 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="clean_dante_ltr" name="DANTE_LTR transposamble elements filtering" version="0.1.4" python_template_version="3.5">
+<tool id="clean_dante_ltr" name="DANTE_LTR transposamble elements filtering" version="0.1.5" python_template_version="3.5">
     <requirements>
 
         <requirement type="package">r-optparse</requirement>
@@ -12,7 +12,16 @@
         &&
         mv output_clean.gff3 $dante_ltr_clean
         &&
-        mv output_RM_lib.fasta $rm_lib
+        mv output_RM_lib_non_redundant.fasta $rm_lib
+        &&
+        mv output_RM_lib_full_TE.fasta $te_full
+        &&
+        mv output_RM_lib_5LTR.fasta $ltr5
+        &&
+        mv output_RM_lib_3LTR.fasta $ltr3
+        &&
+        mv output_summary.pdf $summary
+
     ]]></command>
     <inputs>
         <param type="data" name="dante_ltr" format="gff3" />
@@ -23,6 +32,19 @@
         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"/>
+
+        <data name="te_full" format="fasta" label="Full length LTR transposable
+        elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
+
+        <data name="ltr5" format="fasta" label="5'LTR of transposable
+        elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
+
+        <data name="ltr3" format="fasta" label="3'LTR of transposable
+        elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
+
+        <data name="summary" format="pdf" label="Summary of TE and LTR lenghts based on
+         $dante_ltr.hid and reference $reference.hid"/>
+
     </outputs>
     <help><![CDATA[
         This tool takes output from DANTE_LTR search identifies good quality transposable elements.