Mercurial > repos > petr-novak > dante_ltr
comparison clean_dante_ltr.xml @ 0:7b0bbe7477c4 draft
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
| author | petr-novak |
|---|---|
| date | Tue, 08 Mar 2022 13:24:33 +0000 |
| parents | |
| children | c1498f679b50 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:7b0bbe7477c4 |
|---|---|
| 1 <tool id="clean_dante_ltr" name="DANTE_LTR transposamble elements filtering" version="0.1.0" python_template_version="3.5"> | |
| 2 <requirements> | |
| 3 | |
| 4 <requirement type="package">r-optparse</requirement> | |
| 5 <requirement type="package">blast</requirement> | |
| 6 <requirement type="package">bioconductor-bsgenome</requirement> | |
| 7 <requirement type="package">biocondutor-biostrings</requirement> | |
| 8 <requirement type="package">bioconductor-rtracklayer</requirement> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[ | |
| 11 Rscript ${__tool_directory__}/clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu 32 | |
| 12 && | |
| 13 mv output_clean.gff3 $dante_ltr_clean | |
| 14 && | |
| 15 mv output_RM_lib.fasta $rm_lib | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <param type="data" name="dante_ltr" format="gff3" /> | |
| 19 <param type="data" name="reference" format="fasta" /> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data name="dante_ltr_clean" format="gff3" label="Annotation of validated LTR transposable | |
| 23 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> | |
| 24 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR transposable | |
| 25 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> | |
| 26 </outputs> | |
| 27 <help><![CDATA[ | |
| 28 This tool takes output from DANTE_LTR search identifies good quality transposable elements. | |
| 29 Good quality TE are considered those which does not have any cross-similarity between distinct lineages. | |
| 30 Output from this tool is a annotation in GFF3 format and | |
| 31 non-redundant library of elements for custom RepeatMasker search. | |
| 32 | |
| 33 ]]></help> | |
| 34 </tool> |