Mercurial > repos > petr-novak > dante_ltr

annotate clean_dante_ltr.xml @ 16:7ec262f92d89 draft

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planemo upload commit ba9c740b818bbd5b5a7a5e2afbea827f5bb91419
author petr-novak
date Wed, 10 May 2023 13:07:41 +0000
parents 0ea5d893a057
children d1c3b29b1478
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1 <tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.2.2.4" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="0.2.2.4">dante_ltr</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1}
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7 &&
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8 mv output_clean.gff3 $dante_ltr_clean
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9 &&
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10 mv output_RM_lib_non_redundant.fasta $rm_lib
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11 &&
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12 mv output_RM_lib_full_TE.fasta $te_full
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13 &&
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14 mv output_RM_lib_5LTR.fasta $ltr5
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15 &&
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16 mv output_RM_lib_3LTR.fasta $ltr3
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17 &&
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18 mv output_summary.pdf $summary
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19 ]]></command>
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20 <inputs>
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21 <param type="data" name="dante_ltr" format="gff3"
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22 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
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23 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />
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24 </inputs>
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25 <outputs>
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26 <data name="dante_ltr_clean" format="gff3"
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27 label="Validated LTR retrotransposons annotation (GFF3) based on annotation
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28 $dante_ltr.hid and reference $reference.hid"/>
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29 <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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30
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31 <data name="te_full" format="fasta" label="Library of LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
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33 <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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35 <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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37 <data name="summary" format="pdf" label="LTR retrotransposons lengths summary based on $dante_ltr.hid and reference $reference.hid"/>
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38
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39 </outputs>
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40 <help><![CDATA[
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41 This tool takes output from DANTE_LTR search identifies good quality retrotransposons.
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42 Good quality retrotransposons are considered those which does not have any cross-similarity between distinct lineages.
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43 Output from this tool is a annotation in GFF3 format and
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44 libraries of elements for custom RepeatMasker search.
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45
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46 ]]></help>
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47 </tool>