Mercurial > repos > petr-novak > dante_ltr

annotate clean_dante_ltr.xml @ 5:0c3111ab729b draft

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"planemo upload commit 5a81f1734493a3acf5ff24a573fa2887d92b58a8"
author petr-novak
date Mon, 16 May 2022 07:50:41 +0000
parents 6ae4a341d1f3
children b91ca438a1cb
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1 <tool id="clean_dante_ltr" name="DANTE_LTR transposamble elements filtering" version="0.1.5" 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 <param type="data" name="reference" format="fasta" />
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29 </inputs>
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30 <outputs>
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31 <data name="dante_ltr_clean" format="gff3" label="Annotation of validated LTR transposable
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32 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
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33 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR transposable
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34 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
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36 <data name="te_full" format="fasta" label="Full length LTR transposable
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37 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
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39 <data name="ltr5" format="fasta" label="5'LTR of transposable
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40 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
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42 <data name="ltr3" format="fasta" label="3'LTR of transposable
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43 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
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45 <data name="summary" format="pdf" label="Summary of TE and LTR lenghts based on
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46 $dante_ltr.hid and reference $reference.hid"/>
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47
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48 </outputs>
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49 <help><![CDATA[
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50 This tool takes output from DANTE_LTR search identifies good quality transposable elements.
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51 Good quality TE are considered those which does not have any cross-similarity between distinct lineages.
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52 Output from this tool is a annotation in GFF3 format and
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53 non-redundant library of elements for custom RepeatMasker search.
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54
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55 ]]></help>
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56 </tool>