Mercurial > repos > iuc > te_finder
annotate TEfinder.xml @ 1:2edb80d68a1b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
| author | iuc |
|---|---|
| date | Fri, 23 Sep 2022 11:00:13 +0000 |
| parents | 838fb3a1678f |
| children |
| rev | line source |
|---|---|
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1
2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
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1 <tool id="te_finder" name="TEfinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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
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2 <description>Transposable element insertions finder</description> |
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2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
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3 <macros> |
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2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
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4 <import>macros.xml</import> |
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2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
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5 </macros> |
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2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
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6 <expand macro="xrefs"/> |
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2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
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7 <expand macro="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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8 <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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9 <![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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10 '$__tool_directory__/TEfinder' -fa '$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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11 -alignment '$required_inputs.alignmentFile' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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12 -gtf '$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
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13 -te '$required_inputs.TransposonsToSearch' |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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14 -bamo '$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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15 -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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16 -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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17 -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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18 -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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19 -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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20 #if str( $advanced_options.OutFormat) == "gtf": |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
parents:
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21 -gtfo '$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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22 -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
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23 #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
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24 ]]> |
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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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25 </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:
diff
changeset
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26 |
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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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27 <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:
diff
changeset
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28 <!-- <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:
diff
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29 <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:
diff
changeset
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30 <param name="FastaFile" type="data" format="fasta" label="Select reference genome FASTA index (FA/FASTA file)" /> |
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1
2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
parents:
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31 <param name="alignmentFile" type="data" format="bam,sam" label="Select sample reads aligned to reference genome (BAM/SAM file)" /> |
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2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
parents:
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32 <param name="TransposonsInGenome" type="data" format="gtf,gff" label="Select reference genome TE annotation (GFF/GTF file)" /> |
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2edb80d68a1b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit 5d19bf766a0ac0121ce45b5c532ea5e43825082b
iuc
parents:
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33 <param name="TransposonsToSearch" type="data" format="txt" 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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34 </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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35 <!-- 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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36 <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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37 <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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38 <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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39 <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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40 <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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41 <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
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42 <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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43 </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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44 </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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45 </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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46 |
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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 <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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48 <data format="bed" name="bteinsertion" label="${tool.name} on ${on_string}: BED" /> |
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838fb3a1678f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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49 <data format="gtf" name="gteinsertion" label="${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
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50 <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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51 </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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52 <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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53 </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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54 |
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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 <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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56 <!-- 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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57 <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
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58 <!-- 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
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59 <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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60 <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
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61 <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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62 <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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63 <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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64 <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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65 <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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66 </test> |
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838fb3a1678f
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67 |
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838fb3a1678f
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68 <!-- 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
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69 <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
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70 <!-- 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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71 <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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72 <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
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73 <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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74 <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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75 <param name="OutFormat" value="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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76 <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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77 <output name="gteinsertion" file="TEinsertions.gtf" ftype="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 <output name="discordantreads" file="DiscordantReads.bam" ftype="bam"/> |
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79 </test> |
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80 </tests> |
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81 |
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82 <help> |
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83 <![CDATA[ |
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84 A bioinformatics tool for detecting novel transposable element insertions |
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85 |
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86 Authors: Vista Sohrab & Dilay Hazal Ayhan |
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87 |
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88 TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. |
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89 |
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90 **Output files**:: |
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91 |
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92 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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93 |
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94 TE_insertions.gtf is provided with the same information as the BED file if using -out GTF |
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95 |
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96 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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97 |
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98 **Note**:: |
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99 |
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100 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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101 Modifying the fragment insert size (-fis) based on the sequencing library preparation can be useful. |
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102 |
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103 ]]> |
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104 </help> |
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105 |
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106 <citations> |
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107 <citation type="doi">10.5281/zenodo.4479946</citation> |
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108 </citations> |
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109 |
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110 </tool> |