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planemo upload commit 29868d121127a8bb509a42fb917b09f669ad4a09-dirty
author petr-novak
date Tue, 05 Nov 2024 15:07:08 +0000
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1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="@TOOL_VERSION@" python_template_version="3.5">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="requirements" />
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6 <command detect_errors="exit_code"><![CDATA[
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7 echo \$PATH
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8 &&
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9 dante_ltr --gff3 '$dante'
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10 --reference_sequence '$reference' -M $max_missing --output output --cpu \${GALAXY_SLOTS:-1}
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11 &&
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12 mv output.gff3 $te_ltr_gff
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13 &&
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14 mv output_statistics.csv $statistics
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15 &&
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16 if [ -f output_summary.html ]; then cp output_summary.html $html_report; fi
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17 &&
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18 mkdir -p ${html_report.extra_files_path}
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19 &&
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20 if [ -d output_summary_plots ]; then cp -r output_summary_plots ${html_report.extra_files_path}/; fi
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21 ]]></command>
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22 <inputs>
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23 <param type="data" name="dante" format="gff3" label="GFF3 output from DANTE pipeline - full output"/>
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24 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" />
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25 <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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26 </inputs>
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27 <outputs>
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28 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3)
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29 based on DANTE annotation $dante.hid and reference $reference.hid" />
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30 <data name="statistics" format="tabular" label="LTR retrotransposons detection
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31 summary based on $dante.hid and reference $reference.hid" />
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32 <data name="html_report" format="html" label="LTR retrotransposons detection on $dante.hid and $reference.hid report" />
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33
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34 </outputs>
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35 <help><![CDATA[
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36 This tool uses output from DANTE annotation pipeline to identify full length LTR
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37 transposable elements. Output is in the GFF3 format and include annotation of
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38 5' and 3' Long Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS).
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39
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40 All identified elements contains set of protein domains as defined in
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41 REXdb_. Based on the results of detection of structural features,
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42 elements falls into five categories:
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44 - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP
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45 - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found) rank DLP
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46 - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found) - rank DTL
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47 - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found) - rank DL
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48 - elements as cluster of proteins domains with same classification, no LTRs - rank D
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50 .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1
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51
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52 Principles of detection of LTR retrotransposons is describet in github_ repository of this tool.
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53
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54 .. _github: https://github.com/kavonrtep/dante_ltr
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57 ]]></help>
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58 </tool>