Mercurial > repos > bgruening > racon
annotate racon.xml @ 1:4df02149a270 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
author | bgruening |
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date | Thu, 19 Jul 2018 07:43:14 -0400 |
parents | 51fd3136069d |
children | aa39b19ca11e |
rev | line source |
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1
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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1 <tool id="racon" name="Racon" version="1.3.1.1"> |
0
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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2 <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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3 <macros> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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4 <import>macros.xml</import> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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5 </macros> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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6 <expand macro="requirements" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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7 <version_command>racon --version</version_command> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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8 <command detect_errors="exit_code"><![CDATA[ |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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9 ln -s '$reads' reads.${reads.ext} && |
1
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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10 #if $overlaps.ext == 'sam': |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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11 ln -s '$overlaps' overlaps.${overlaps.ext} && |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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12 #else: |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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13 ln -s '$overlaps' overlaps.paf && |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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14 #end if |
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51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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15 ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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16 |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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17 racon |
1
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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18 reads.${reads.ext} |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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19 #if $overlaps.ext == 'sam': |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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20 overlaps.${overlaps.ext} |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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21 #else: |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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22 overlaps.paf |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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23 #end if |
0
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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24 corrected_reads.${corrected_reads.ext} |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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25 -t \${GALAXY_SLOTS:-4} |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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26 $u |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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27 $f |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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28 -w $w |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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29 -q $q |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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30 -e $e |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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31 -m $m |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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32 -x $x |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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33 -g $g |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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34 > racon_polished_consensus.fa |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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35 ]]></command> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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36 <inputs> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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37 <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/> |
1
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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38 <param type="data" name="overlaps" format="sam,interval" label="Overlaps"/> |
0
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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39 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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40 |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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41 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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42 <param argument="-f" type="boolean" truevalue="-f" falsevalue="" label="perform fragment correction instead of contig polishing" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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43 <param argument="-w" type="integer" value="500" label="Size of window on which POA is performed" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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44 <param argument="-q" type="float" value="10.0" label="Threshold for average base quality of windows used in poa" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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45 <param argument="-e" type="float" value="0.3" label="Maximum allowed error rate used for filtering overlaps" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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46 <param argument="-m" type="integer" value="5" label="Score for matching bases" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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47 <param argument="-x" type="integer" value="-4" label="Score for mismatching bases" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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48 <param argument="-g" type="integer" value="-8" max="0" label="Gap penalty" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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49 |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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50 </inputs> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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51 <outputs> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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52 <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" /> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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53 </outputs> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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54 <tests> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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55 <test> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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56 <param name="reads" ftype="fasta" value="sample_reads.fasta"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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57 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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58 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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59 <param name="u" value="true"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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60 <param name="f" value="true"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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61 <param name="w" value="800"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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62 <param name="e" value="0.2"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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63 <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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64 </test> |
1
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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65 <test> |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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66 <param name="reads" ftype="fasta" value="sample_reads.fasta"/> |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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67 <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/> |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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68 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/> |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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69 <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/> |
4df02149a270
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
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70 </test> |
0
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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71 </tests> |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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72 <help><![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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73 |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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74 **What it does** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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75 |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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76 Consensus module for raw de novo DNA assembly of long uncorrected reads. |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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77 |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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78 Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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79 which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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80 or better quality compared to the output generated by assembly methods which employ both error correction |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
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81 and consensus steps, while providing a speedup of several times compared to those methods. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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82 It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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83 |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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84 Racon can be used as a polishing tool after the assembly with either Illumina data or data |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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85 produced by third generation of sequencing. The type of data inputed is automatically detected. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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86 |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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87 Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ |
51fd3136069d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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88 format and overlaps/alignments between the reads and the contigs in SAM format. Output is a set of polished contigs in FASTA format printed to stdout. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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89 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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90 Racon can also be used as a read error-correction tool. In this scenario, the SAM file needs |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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91 to contain pairwise overlaps between reads including dual overlaps. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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92 |
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93 ]]></help> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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94 <expand macro="citations" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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95 </tool> |