Mercurial > repos > petr-novak > dante_ltr
diff clean_dante_ltr.xml @ 3:6ae4a341d1f3 draft
"planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
author | petr-novak |
---|---|
date | Tue, 03 May 2022 12:38:12 +0000 |
parents | f131886ea194 |
children | b91ca438a1cb |
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--- 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.