Mercurial > repos > iuc > te_finder
annotate TEfinder.xml @ 0:838fb3a1678f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
| author | iuc |
|---|---|
| date | Mon, 08 Aug 2022 19:41:18 +0000 |
| parents | |
| children | 2edb80d68a1b |
| rev | line source |
|---|---|
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0
838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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changeset
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1 <tool id="te_finder" name="TEfinder" version="1.0.1" profile="21.05"> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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2 <description>Transposable element insertions finder</description> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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3 |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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4 <requirements> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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5 <requirement type="package" version="1.15.1">samtools</requirement> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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6 <requirement type="package" version="2.30.0">bedtools</requirement> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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7 <requirement type="package" version="2.27.4">picard</requirement> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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8 <requirement type="package" version="3.4">grep</requirement> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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9 <requirement type="package" version="1.07.1">bc</requirement> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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10 </requirements> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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11 |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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12 <command> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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13 <![CDATA[ |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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14 '$__tool_directory__/TEfinder' -fa '$required_inputs.FastaFile' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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15 -alignment '$required_inputs.alignmentFile' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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16 -gtf '$required_inputs.TransposonsInGenome' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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17 -te '$required_inputs.TransposonsToSearch' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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18 -bamo '$discordantreads' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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19 -bedo '$bteinsertion' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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20 -threads '\${GALAXY_SLOTS:-1}' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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21 -fis $($advanced_options.FragmentInsertSize) |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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22 -md $($advanced_options.MaxDistanceForMerge) |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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23 -k $($advanced_options.MaxTSDLength) |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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24 #if str( $advanced_options.OutFormat) == "gtf": |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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25 -gtfo '$gteinsertion' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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26 -out $($advanced_options.OutFormat) |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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27 #end if |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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28 ]]> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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29 </command> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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30 |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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31 <inputs> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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changeset
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32 <!-- <param format="fasta" name="input" type="data" label="Source file"/> --> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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33 <section name="required_inputs" title="Required Inputs" expanded="True"> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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34 <param name="FastaFile" type="data" format="fasta" label="Select reference genome FASTA index (FA/FASTA file)" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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changeset
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35 <param name="alignmentFile" type="data" format="bam" label="Select sample reads aligned to reference genome (BAM/SAM file)" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
diff
changeset
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36 <param name="TransposonsInGenome" type="data" format="gtf" label="Select reference genome TE annotation (GFF/GTF file)" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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37 <param name="TransposonsToSearch" type="data" format="text" label="Select TE names" help="Single column text file" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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38 </section> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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39 <!-- Advanced Options --> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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40 <section name="advanced_options" title="Advanced Options" expanded="False"> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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41 <param name="FragmentInsertSize" argument="-fis" type="integer" min="0" value="400" label="Short-read sequencing fragment insert size" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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42 <param name="MaxDistanceForMerge" argument="-md" type="integer" min="0" value="150" label="Maximum distance between reads for bedtools merge" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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43 <param name="MaxTSDLength" argument="-k" type="integer" min="0" value="20" label="Maximum TE target site duplication (TSD) length" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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44 <param name="OutFormat" argument="-out" type="select" display="radio" label="Select output format as BED [GTF]" help="See help below for more details"> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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45 <option value="bed" selected="True">Default format is BED</option> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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46 <option value="gtf">Other available format is GTF (-out gtf)</option> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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47 </param> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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48 </section> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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49 </inputs> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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50 |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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51 <outputs> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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52 <data format="bed" name="bteinsertion" label="${tool.name} on ${on_string}: BED" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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53 <data format="gtf" name="gteinsertion" label="${tool.name} on ${on_string}: GTF"> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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54 <filter>advanced_options['OutFormat'] and 'gtf' in advanced_options['OutFormat']</filter> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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55 </data> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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56 <data format="bam" name="discordantreads" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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57 </outputs> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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58 |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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59 <tests> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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60 <!-- Test for the most simple case for BED output : Running TEfinder with a .bam file and a .fasta file --> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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61 <test expect_num_outputs="2"> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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62 <!-- TEfinder commands: TEfinder -alignment sample.bam -fa reference.fa -gtf TEs.gtf -te List_of_TEs.txt --> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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63 <param name="FastaFile" ftype="fasta" value="reference.fa"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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64 <param name="alignmentFile" ftype="bam" value="sample.bam"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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65 <param name="TransposonsInGenome" ftype="gtf" value="TEs.gtf"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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66 <param name="TransposonsToSearch" ftype="txt" value="List_of_TEs.txt"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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67 <param name="OutFormat" value="bed" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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68 <output name="bteinsertion" file="TEinsertions.bed" ftype="bed"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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69 <output name="discordantreads" file="DiscordantReads.bam" ftype="bam"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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70 </test> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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71 |
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838fb3a1678f
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72 <!-- Test for the GTF output --> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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73 <test expect_num_outputs="3"> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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74 <!-- TEfinder commands: TEfinder -alignment sample.bam -fa reference.fa -gtf TEs.gtf -te List_of_TEs.txt -out gtf --> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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75 <param name="FastaFile" ftype="fasta" value="reference.fa"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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76 <param name="alignmentFile" ftype="bam" value="sample.bam"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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77 <param name="TransposonsInGenome" ftype="gtf" value="TEs.gtf"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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78 <param name="TransposonsToSearch" ftype="txt" value="List_of_TEs.txt"/> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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79 <param name="OutFormat" value="gtf" /> |
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80 <output name="bteinsertion" file="TEinsertions.bed" ftype="bed"/> |
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81 <output name="gteinsertion" file="TEinsertions.gtf" ftype="gtf"/> |
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82 <output name="discordantreads" file="DiscordantReads.bam" ftype="bam"/> |
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83 </test> |
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84 </tests> |
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85 |
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86 <help> |
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87 <![CDATA[ |
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88 A bioinformatics tool for detecting novel transposable element insertions |
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89 |
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90 Authors: Vista Sohrab & Dilay Hazal Ayhan |
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91 |
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92 TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. |
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93 |
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94 **Output files**:: |
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95 |
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96 TE_insertions.bed contains identified TE insertion events in sample (in the final column, FILTER attribute with "PASS" refers to high confidence insertion events while instances labeled as "in_repeat", "weak_evidence", "strand bias" or a combination of these three labels indicate less confident insertion events) |
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97 |
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98 TE_insertions.gtf is provided with the same information as the BED file if using -out GTF |
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99 |
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100 DiscordantReads.bam contains all discordant reads that have been identified based on the TEs of interest that have been submitted to TEfinder |
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101 |
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102 **Note**:: |
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103 |
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104 Modifying the maximum TSD length (-k) could be useful if there is an unexpected number of insertion events identified with the default parameter. The optimal maximum TSD length can vary across datasets. |
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105 Modifying the fragment insert size (-fis) based on the sequencing library preparation can be useful. |
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106 |
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107 ]]> |
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108 </help> |
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109 |
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110 <citations> |
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111 <citation type="doi">10.5281/zenodo.4479946</citation> |
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112 </citations> |
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113 |
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114 </tool> |