Mercurial > repos > petr-novak > dante_ltr

annotate clean_dante_ltr.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="clean_dante_ltr" name="DANTE_LTR transposamble elements filtering" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3
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4 <requirement type="package">r-optparse</requirement>
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5 <requirement type="package">blast</requirement>
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6 <requirement type="package">bioconductor-bsgenome</requirement>
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7 <requirement type="package">biocondutor-biostrings</requirement>
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8 <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 ${__tool_directory__}/clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu 32
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12 &&
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13 mv output_clean.gff3 $dante_ltr_clean
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14 &&
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15 mv output_RM_lib.fasta $rm_lib
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16 ]]></command>
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17 <inputs>
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18 <param type="data" name="dante_ltr" format="gff3" />
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19 <param type="data" name="reference" format="fasta" />
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20 </inputs>
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21 <outputs>
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22 <data name="dante_ltr_clean" format="gff3" label="Annotation of validated LTR transposable
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23 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
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24 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR transposable
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25 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
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26 </outputs>
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27 <help><![CDATA[
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28 This tool takes output from DANTE_LTR search identifies good quality transposable elements.
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29 Good quality TE are considered those which does not have any cross-similarity between distinct lineages.
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30 Output from this tool is a annotation in GFF3 format and
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31 non-redundant library of elements for custom RepeatMasker search.
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32
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33 ]]></help>
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34 </tool>