Mercurial > repos > petr-novak > dante_ltr

annotate clean_dante_ltr.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="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.1.6.1" 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">bioconductor-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_non_redundant.fasta $rm_lib
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16 &&
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17 mv output_RM_lib_full_TE.fasta $te_full
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18 &&
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19 mv output_RM_lib_5LTR.fasta $ltr5
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20 &&
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21 mv output_RM_lib_3LTR.fasta $ltr3
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22 &&
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23 mv output_summary.pdf $summary
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24
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25 ]]></command>
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26 <inputs>
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27 <param type="data" name="dante_ltr" format="gff3"
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28 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
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29 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />
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30 </inputs>
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31 <outputs>
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32 <data name="dante_ltr_clean" format="gff3"
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33 label="Validated LTR retrotransposons annotation (GFF3) based on annotation
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34 $dante_ltr.hid and reference $reference.hid"/>
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35 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
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37 <data name="te_full" format="fasta" label="Library of full length LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
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38
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39 <data name="ltr5" format="fasta" label="Library of 5'LTR of retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
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41 <data name="ltr3" format="fasta" label="Library of 3'LTR of retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
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43 <data name="summary" format="pdf" label="LTR retrotransposons lengths summary based on $dante_ltr.hid and reference $reference.hid"/>
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44
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45 </outputs>
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46 <help><![CDATA[
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47 This tool takes output from DANTE_LTR search identifies good quality retrotransposons.
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48 Good quality retrotransposons are considered those which does not have any cross-similarity between distinct lineages.
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49 Output from this tool is a annotation in GFF3 format and
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50 libraries of elements for custom RepeatMasker search.
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52 ]]></help>
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53 </tool>