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planemo upload commit 29868d121127a8bb509a42fb917b09f669ad4a09-dirty
author petr-novak
date Tue, 05 Nov 2024 15:07:08 +0000
parents d1c3b29b1478
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1 <tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" 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 clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1}
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8 &&
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9 mv output_clean.gff3 $dante_ltr_clean
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10 &&
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11 mv output_RM_lib_non_redundant.fasta $rm_lib
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12 &&
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13 mv output_RM_lib_full_TE.fasta $te_full
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14 &&
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15 mv output_RM_lib_5LTR.fasta $ltr5
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16 &&
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17 mv output_RM_lib_3LTR.fasta $ltr3
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18 &&
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19 mv output_summary.pdf $summary
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20 ]]></command>
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21 <inputs>
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22 <param type="data" name="dante_ltr" format="gff3"
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23 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
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24 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />
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25 </inputs>
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26 <outputs>
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27 <data name="dante_ltr_clean" format="gff3"
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28 label="Validated LTR retrotransposons annotation (GFF3) based on annotation
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29 $dante_ltr.hid and reference $reference.hid"/>
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30 <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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31
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32 <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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34 <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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36 <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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38 <data name="summary" format="pdf" label="LTR retrotransposons lengths summary based on $dante_ltr.hid and reference $reference.hid"/>
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39
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40 </outputs>
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41 <help><![CDATA[
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42 This tool takes output from DANTE_LTR search identifies good quality retrotransposons.
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43 Good quality retrotransposons are considered those which does not have any cross-similarity between distinct lineages.
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44 Output from this tool is a annotation in GFF3 format and
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45 libraries of elements for custom RepeatMasker search.
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46
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47 ]]></help>
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48 </tool>