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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/canu commit da020fbee6e2bd91bc4a8d0850dc601db34ac82b-dirty
author jdv
date Sun, 15 Oct 2017 22:29:50 -0400
parents ed5df116fad3
children
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1 <tool id="canu" name="Canu" version="1.6">
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3 <description>Assembler optimized for long error-prone reads</description>
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5 <!-- ***************************************************************** -->
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7 <!--
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8 <requirements>
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9 <requirement type="package" version="1.6">canu</requirement>
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10 </requirements>
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11 -->
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13 <!-- ***************************************************************** -->
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15 <version_command>canu --version | perl -wnE'print "$1\n" for /^Canu (?:snapshot v)?(\S+)/g'</version_command>
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18 <!-- ***************************************************************** -->
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20 <command detect_errors="aggressive">
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21 <![CDATA[
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23 canu
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25 -p canu_galaxy
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26 -d out_dir
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27 useGrid=false
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28 genomeSize=$genomeSize
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29 rawErrorRate=$rawErrorRate
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30 correctedErrorRate=$correctedErrorRate
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31 minReadLength=$minReadLength
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32 minOverlapLength=$minOverlapLength
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33 corOutCoverage=$corOutCoverage
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34 contigFilter="
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35 ${contigFilter.minReads}
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36 ${contigFilter.minLength}
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37 ${contigFilter.singleReadSpan}
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38 ${contigFilter.lowCovSpan}
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39 ${contigFilter.lowCovDepth}
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40 "
0
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41 minThreads=\${GALAXY_SLOTS:-1}
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42 maxThreads=\${GALAXY_SLOTS:-1}
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43 gnuplotTested=true
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44 useGrid=false
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45 $mode
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46 $input
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49 ]]>
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50 </command>
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52 <!-- ***************************************************************** -->
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54 <inputs>
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55
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56 <param name="input" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Input reads" />
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57 <param name="mode" type="select">
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58 <option value="-nanopore-raw" selected="true">nanopore raw</option>
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59 <option value="-pacbio-raw">pacbio raw</option>
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60 <option value="-nanopore-corrected">nanopore corrected</option>
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61 <option value="-pacbio-corrected">pacbio corrected</option>
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62 </param>
1
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63 <param argument="genomeSize" type="text" size="5" label="Estimated genome size (e.g. 80m, 15k, 2g)" />
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64 <param argument="rawErrorRate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" />
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65 <param argument="correctedErrorRate" type="float" value="0.144" min="0" max="1" size="5" label="Maximum corrected overlap mismatch (0-1)" />
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66 <param argument="minReadLength" type="integer" value="1000" min="1" size="5" label="Minimum read length" />
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67 <param argument="minOverlapLength" type="integer" value="500" min="1" size="5" label="Minimum overlap" />
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68 <param argument="corOutCoverage" type="integer" value="40" min="1" size="5" label="Target coverage for corrected reads" />
0
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69
2
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70 <section name="contigFilter" title="Contig Filters">
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71 <param argument="minReads" type="integer" value="2" min="0" label="Minimum reads" />
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72 <param argument="minLength" type="integer" value="0" min="0" label="Minimum length" />
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73 <param argument="singleReadSpan" type="float" value="1.0" min="0.0" max="1.0" label="Maximum single read span (fraction)" />
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74 <param argument="lowCovSpan" type="float" value="0.5" min="0.0" max="1.0" label="Low coverage span (fraction)" />
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75 <param argument="lowCovDepth" type="integer" value="5" min="0" label="Low coverage depth" />
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76 </section>
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77
0
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78 </inputs>
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80 <!-- ***************************************************************** -->
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82 <outputs>
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84 <data name="contigs" format="fasta" from_work_dir="out_dir/canu_galaxy.contigs.fasta" label="${tool.name} on ${on_string} (contigs)" />
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85 <data name="unitigs" format="fasta" from_work_dir="out_dir/canu_galaxy.unitigs.fasta" label="${tool.name} on ${on_string} (unitigs)" />
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86
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87 </outputs>
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88
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89 <!-- ***************************************************************** -->
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91 <tests>
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92 </tests>
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94 <!-- ***************************************************************** -->
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96 <help>
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97 <![CDATA[
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99 **Description**
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101 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
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102 sequencing data. Nanopolish can calculate an improved consensus sequence for a
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103 draft genome assembly, detect base modifications, call SNPs and indels with
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104 respect to a reference genome and more.
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106 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
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107 as input, such as can be produced by `poretools combine`, and always outputs a
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108 single FASTQ file.
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110 This is the `extract` module.
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112 ]]>
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113 </help>
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115 <!-- ***************************************************************** -->
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117 <citations>
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118 </citations>
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120 </tool>