Mercurial > repos > petr-novak > dante_ltr

annotate dante_ltr_search.xml @ 0:7b0bbe7477c4 draft

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"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
author petr-novak
date Tue, 08 Mar 2022 13:24:33 +0000
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1 <tool id="dante_ltr_search" name="DANTE_LTR transposable element identification" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package">blast</requirement>
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4 <requirement type="package">r-optparse</requirement>
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5 <requirement type="package">bioconductor-bsgenome</requirement>
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6 <requirement type="package">biocondutor-biostrings</requirement>
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7 <requirement type="package">bioconductor-rtracklayer</requirement>
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8
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 Rscript ${__tool_directory__}/extract_putative_ltr.R --gff3 '$dante' --reference_sequence '$reference' --output output --cpu 32
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12 &&
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13 mv output.gff3 $te_ltr_gff
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14 ]]></command>
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15 <inputs>
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16 <param type="data" name="dante" format="gff3" label="Filtered gff3 output from DANTE pipeline"/>
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17 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" />
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18 </inputs>
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19 <outputs>
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20 <data name="te_ltr_gff" format="gff3" label="Annotation of detected LTR transposable elements
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21 based on the annotation $dante.hid and reference $reference.hid" />
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22 </outputs>
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23 <help><![CDATA[
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24 This tool uses output from DANTE annotation pipeline to identify full length LTR
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25 transposable elements. Output is in the GFF3 format and include annotation of
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26 5' and 3' Longe Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS).
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27
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28 All identified elements contains complete set of protein domains as defined in
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29 REXdb_. Based on the results detection structural feature,
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30 elements falls into four categories:
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31
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32 - elements with domains, 5'LTR, 3'LTR, TSD and PBS
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33 - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found)
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34 - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found)
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35 - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found)
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36
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37 .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1
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38
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39 ]]></help>
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40 </tool>