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annotate racon.xml @ 0:51fd3136069d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
author bgruening
date Mon, 11 Jun 2018 16:47:50 -0400
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51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
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1 <tool id="racon" name="Racon" version="1.3.1">
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2 <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <version_command>racon --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$reads' reads.${reads.ext} &&
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10 ln -s '$overlaps' overlaps.${overlaps.ext} &&
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11 ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} &&
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12
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13 racon
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14 reads.${reads.ext}
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15 overlaps.${overlaps.ext}
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16 corrected_reads.${corrected_reads.ext}
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17 -t \${GALAXY_SLOTS:-4}
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18 $u
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19 $f
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20 -w $w
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21 -q $q
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22 -e $e
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23 -m $m
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24 -x $x
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25 -g $g
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26 > racon_polished_consensus.fa
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27 ]]></command>
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28 <inputs>
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29 <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/>
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30 <param type="data" name="overlaps" format="sam" label="Overlaps"/>
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31 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/>
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32
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33 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" />
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34 <param argument="-f" type="boolean" truevalue="-f" falsevalue="" label="perform fragment correction instead of contig polishing" />
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35 <param argument="-w" type="integer" value="500" label="Size of window on which POA is performed" />
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36 <param argument="-q" type="float" value="10.0" label="Threshold for average base quality of windows used in poa" />
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37 <param argument="-e" type="float" value="0.3" label="Maximum allowed error rate used for filtering overlaps" />
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38 <param argument="-m" type="integer" value="5" label="Score for matching bases" />
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39 <param argument="-x" type="integer" value="-4" label="Score for mismatching bases" />
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40 <param argument="-g" type="integer" value="-8" max="0" label="Gap penalty" />
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41
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42 </inputs>
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43 <outputs>
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44 <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
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49 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
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50 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
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51 <param name="u" value="true"/>
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52 <param name="f" value="true"/>
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53 <param name="w" value="800"/>
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54 <param name="e" value="0.2"/>
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55 <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59
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60 **What it does**
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61
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62 Consensus module for raw de novo DNA assembly of long uncorrected reads.
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63
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64 Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods
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65 which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar
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66 or better quality compared to the output generated by assembly methods which employ both error correction
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67 and consensus steps, while providing a speedup of several times compared to those methods.
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68 It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
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69
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70 Racon can be used as a polishing tool after the assembly with either Illumina data or data
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71 produced by third generation of sequencing. The type of data inputed is automatically detected.
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72
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73 Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ
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74 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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75
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76 Racon can also be used as a read error-correction tool. In this scenario, the SAM file needs
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77 to contain pairwise overlaps between reads including dual overlaps.
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78
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79 ]]></help>
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80 <expand macro="citations" />
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81 </tool>