Mercurial > repos > petr-novak > dante_ltr

annotate dante_ltr_search.xml @ 9:1aa578e6c8b3 draft

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"planemo upload commit 9488b982bae902f1868785ec4ad47134dac50ff3"
author petr-novak
date Wed, 29 Jun 2022 09:25:54 +0000
parents 9de392f2fc02
children ff01d4263391
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1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.6.1" 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">bioconductor-biostrings</requirement>
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7 <requirement type="package">bioconductor-rtracklayer</requirement>
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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' -M $max_missing --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 &&
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15 mv output_statistics.csv $statistics
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16 ]]></command>
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17 <inputs>
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18 <param type="data" name="dante" format="gff3" label="Filtered GFF3 output from DANTE pipeline"/>
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19 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" />
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20 <param type="integer" name="max_missing" min="0" max="3" value="1" label="Maximum number of missing protein domains to tolerate in full length retrotransposon" />
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21 </inputs>
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22 <outputs>
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23 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3)
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24 based on DANTE annotation $dante.hid and reference $reference.hid" />
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25 <data name="statistics" format="tabular" label="LTR retrotransposons detection
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26 summary based on $dante.hid and reference $reference.hid" />
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27 </outputs>
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28 <help><![CDATA[
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29 This tool uses output from DANTE annotation pipeline to identify full length LTR
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30 transposable elements. Output is in the GFF3 format and include annotation of
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31 5' and 3' Long Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS).
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33 All identified elements contains set of protein domains as defined in
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34 REXdb_.Based on the results of detection of structural features,
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35 elements falls into five categories:
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37 - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP
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38 - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found) rank DLP
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39 - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found) - rank DTL
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40 - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found) - rank DL
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41 - elements as cluster of proteins domains with same classification, no LTRs - rank D
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43 .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1
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45 ]]></help>
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46 </tool>