Mercurial > repos > petr-novak > dante_ltr
view clean_dante_ltr.xml @ 14:3b3a87915ef6 draft
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
author | petr-novak |
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date | Mon, 30 Jan 2023 10:05:47 +0000 |
parents | 559940c04c44 |
children | 0ea5d893a057 |
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<tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.2.2.0" python_template_version="3.5"> <requirements> <requirement type="package">dante_ltr=0.2.2.0</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1} && mv output_clean.gff3 $dante_ltr_clean && 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" label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/> <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" /> </inputs> <outputs> <data name="dante_ltr_clean" format="gff3" label="Validated LTR retrotransposons annotation (GFF3) based on annotation $dante_ltr.hid and reference $reference.hid"/> <data name="rm_lib" format="fasta" label="Non-redundant library of LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/> <data name="te_full" format="fasta" label="Library of LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/> <data name="ltr5" format="fasta" label="Library of 5'LTR of retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/> <data name="ltr3" format="fasta" label="Library of 3'LTR of retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/> <data name="summary" format="pdf" label="LTR retrotransposons lengths summary based on $dante_ltr.hid and reference $reference.hid"/> </outputs> <help><![CDATA[ This tool takes output from DANTE_LTR search identifies good quality retrotransposons. Good quality retrotransposons are considered those which does not have any cross-similarity between distinct lineages. Output from this tool is a annotation in GFF3 format and libraries of elements for custom RepeatMasker search. ]]></help> </tool>