Mercurial > repos > petr-novak > dante_ltr
diff clean_dante_ltr.xml @ 0:7b0bbe7477c4 draft
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
author | petr-novak |
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date | Tue, 08 Mar 2022 13:24:33 +0000 |
parents | |
children | c1498f679b50 |
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--- /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> \ No newline at end of file