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annotate racon.xml @ 9:936f0b5e7fcc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 2ac6111065e4c2ad30947819faabfc8439762354
author bgruening
date Sun, 27 Aug 2023 08:47:31 +0000
parents e100a765370e
children 78c533842eeb
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936f0b5e7fcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 2ac6111065e4c2ad30947819faabfc8439762354
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1 <tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
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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 #if $reads.ext.startswith("fasta")
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10 #set ext="fasta"
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11 #else
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12 #set ext="fastq"
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13 #end if
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14 #if $reads.ext.endswith(".gz")
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15 #set ext=ext+".gz"
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16 #end if
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17
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18 ln -s '$reads' reads.$ext &&
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19 #if $overlaps.ext == 'sam':
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20 ln -s '$overlaps' overlaps.${overlaps.ext} &&
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21 #else:
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22 ln -s '$overlaps' overlaps.paf &&
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23 #end if
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25 #if $corrected_reads.ext.startswith("fasta")
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26 #set cext="fasta"
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27 #else
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28 #set cext="fastq"
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29 #end if
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30 #if $corrected_reads.ext.endswith(".gz")
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31 #set cext=cext+".gz"
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32 #end if
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33 ln -s '$corrected_reads' corrected_reads.$cext &&
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34
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35 racon
4
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36 reads.$ext
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37 #if $overlaps.ext == 'sam':
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38 overlaps.${overlaps.ext}
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39 #else:
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40 overlaps.paf
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41 #end if
4
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42 corrected_reads.$cext
0
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43 -t \${GALAXY_SLOTS:-4}
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44 $include_unpolished
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45 $fragment_correction
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46 -w $window_length
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47 -q $quality_threshold
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48 -e $error_threshold
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49 $no_trimming
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50 -m $match
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51 -x $mismatch
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52 -g $gap
0
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53 > racon_polished_consensus.fa
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54 ]]></command>
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55 <inputs>
8
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56 <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences" help="input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences used for correction"/>
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57 <param type="data" name="overlaps" format="paf,sam,tabular" label="Overlaps" help="input file in MHAP/PAF/SAM format (can be compressed with gzip) containing overlaps between sequences and target sequences"/>
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58 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences" help="Input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences which will be corrected"/>
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59 <param argument="--include-unpolished" type="boolean" truevalue="-u" falsevalue="" label="Include unpolished" help="Output unpolished target sequences" />
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60 <param argument="--fragment-correction" type="boolean" truevalue="-f" falsevalue="" label="Fragment correction" help="Perform fragment correction instead of contig polishing. Note: overlaps file should contain dual/self overlaps" />
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61 <param argument="--window-length" type="integer" value="500" label="Window length" help="Size of window on which POA is performed"/>
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62 <param argument="--quality-threshold" type="float" min="0" value="10.0" label="Quality threshold" help="Threshold for average base quality of windows used in POA"/>
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63 <param argument="--error-threshold" type="float" min="0" value="0.3" label="Error threshold" help="Maximum allowed error rate used for filtering overlaps" />
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64 <param argument="--no-trimming" type="boolean" truevalue="--no-trimming" falsevalue="" checked="false" label="No trimming" help="Disables consensus trimming at window ends" />
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65 <param argument="--match" type="integer" value="3" label="Match score" help="Score for matching bases. Defalt: 3" />
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66 <param argument="--mismatch" type="integer" value="-5" label="Mismatch score" help="Score for mismatching bases. Default: -5" />
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67 <param argument="--gap" type="integer" value="-4" max="0" label="Gap penalty" />
0
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68 </inputs>
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69 <outputs>
8
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70 <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" label="${tool.name} on ${on_string}: consensus sequence"/>
0
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71 </outputs>
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72 <tests>
8
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73 <test expect_num_outputs="1">
0
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74 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
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75 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
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76 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
8
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77 <param name="include_unpolished" value="true"/>
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78 <param name="fragment_correction" value="true"/>
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79 <param name="window_length" value="800"/>
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80 <param name="error_threshold" value="0.2"/>
0
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81 <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
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82 </test>
8
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83 <test expect_num_outputs="1">
1
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84 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
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85 <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/>
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86 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
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87 <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/>
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88 </test>
8
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89 <test expect_num_outputs="1">
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90 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
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91 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
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92 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
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93 <param name="include_unpolished" value="false"/>
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94 <param name="fragment_correction" value="false"/>
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95 <param name="quality_threshold" value="9.0"/>
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96 <param name="no_trimming" value="true"/>
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97 <param name="match" value="7"/>
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98 <param name="mismatch" value="-4"/>
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99 <param name="gap" value="-3"/>
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100 <output name="consensus" ftype="fasta" file="consensus_result1.fasta"/>
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101 </test>
0
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102 </tests>
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103 <help><![CDATA[
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104
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105 **What it does**
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106
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107 Consensus module for raw de novo DNA assembly of long uncorrected reads.
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108
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109 Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods
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110 which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar
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111 or better quality compared to the output generated by assembly methods which employ both error correction
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112 and consensus steps, while providing a speedup of several times compared to those methods.
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113 It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
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114
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115 Racon can be used as a polishing tool after the assembly with either Illumina data or data
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116 produced by third generation of sequencing. The type of data inputed is automatically detected.
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117
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118 Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ
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119 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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120
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121 Racon can also be used as a read error-correction tool. In this scenario, the SAM file needs
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122 to contain pairwise overlaps between reads including dual overlaps.
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123
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124 ]]></help>
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125 <expand macro="citations" />
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126 </tool>