Mercurial > repos > bgruening > nanopolish_variants

annotate nanopolish_variants.xml @ 3:bc79b5b0fe04 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
author bgruening
date Wed, 19 Jun 2019 03:46:05 -0400
parents 1ebed8b65752
children de5b3d8f5b90
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1 <tool id="nanopolish_variants" name="Nanopolish variants" version="0.1.0">
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2 <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</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 <command detect_errors="exit_code"><![CDATA[
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8 ln -s '$input_merged' reads.fasta &&
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9
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10 #if $input_reads_raw.extension == 'fast5':
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11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
3
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12
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
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13 #else if $input_reads_raw.extension == 'fast5.tar':
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
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14 ln -s '$input_reads_raw' fast5_files.tar &&
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15 mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
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17 #else if $input_reads_raw.extension == 'fast5.tar.bz2':
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18 ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
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19 mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
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20
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21 #else:
0
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22 ln -s '$input_reads_raw' fast5_files.tar.gz &&
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23 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
3
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24
0
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25 #end if
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26
3
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27 nanopolish index
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28 -d fast5_files/
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29 #if $adv.input_seq_summary:
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30 -s '$adv.input_seq_summary'
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31 #end if
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32 reads.fasta &&
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33
0
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34 ln -s '$b' reads.bam &&
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35 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
1
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36 #if $reference_source.reference_source_selector == 'history':
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37 ln -f -s '$reference_source.ref_file' genome.fa &&
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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38 #else:
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39 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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40 #end if
0
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41
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42 nanopolish variants
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43 -r reads.fasta
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44 -b reads.bam
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45 -g genome.fa
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46 -o variants.vcf
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47 #if $consensus:
3
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48 --consensus
0
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49 #end if
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50
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51 $snps
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52 $verbose
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53 $homopolymer
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54 $faster
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55 $all_bases
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56
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57 -m $min_candidate_frequency
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58 -d $min_candidate_depth
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59 -x $max_haplotypes
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60 --max-rounds $max_rounds
1
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61 --threads "\${GALAXY_SLOTS:-4}"
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62 #if str($min_flanking_sequence):
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63 --min-flanking-sequence $min_flanking_sequence
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64 #end if
0
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65 #if $ploidy != -1:
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66 --ploidy $ploidy
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67 #end if
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68
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69 #if $w and str($w).strip():
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70 -w "${w}"
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71 #end if
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72 #if $methylation_aware and str($methylation_aware).strip():
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73 -q "${methylation_aware}"
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74 #end if
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75
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76 #if $adv.input_events_bam:
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77 -e '$adv.input_events_bam'
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78 #end if
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79 #if $adv.input_genotype:
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80 --genotype '$adv.input_genotype'
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81 #end if
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82 #if $adv.input_candidates:
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83 -c '$adv.input_candidates'
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84 #end if
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85 #if $adv.input_alt_bc_bam:
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86 -a '$adv.input_alt_bc_bam'
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87 #end if
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88 #if $adv.input_models_fofn:
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89 --models-fofn '$input_models_fofn'
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90 #end if
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91
3
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92 &&
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93
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94 nanopolish vcf2fasta --skip-checks -g genome.fa variants.vcf > polished.fa
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95
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96
0
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97 ]]></command>
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98 <inputs>
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99 <!-- index inputs -->
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100 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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101 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
0
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102
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103 <!-- variants consensus inputs -->
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104 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
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105 <conditional name="reference_source">
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106 <param name="reference_source_selector" type="select" label="Load reference genome from">
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107 <option value="cached">Local cache</option>
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108 <option value="history">History</option>
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109 </param>
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110 <when value="cached">
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111 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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112 <options from_data_table="all_fasta">
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113 </options>
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114 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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115 </param>
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116 </when>
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117 <when value="history">
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118 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
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119 </when>
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120 </conditional>
0
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121
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122 <section name="adv" title="Optional data inputs">
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123 <!-- optional inputs -->
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124 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
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125 <param type="data" name="input_events_bam" format="bam" optional="true" label="Events aligned to the reference genome" help="(-e)" />
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126 <param type="data" name="input_genotype" format="vcf" optional="true" label="Call genotypes for the variants in the vcf file" help="(--genotype)" />
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127 <param type="data" name="input_candidates" format="vcf" optional="true"
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128 label="Use variant candidates, rather than discovering them from aligned reads" help="(-c)" />
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129 <param type="data" name="input_alt_bc_bam" format="bam" optional="true" label="Alternative basecaller used that does not output event annotations" help="(-a)" />
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130 <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" />
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131 </section>
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132
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133 <!-- optional params -->
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134 <!-- optional params -->
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135 <param argument="-w" type="text" optional="true"
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136 label="find variants in window of region chromsome:start-end" />
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137 <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/>
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138 <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/>
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139 <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/>
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140 <param name="max_haplotypes" type="integer" optional="true" value="1000" label="Consider at most N haplotype combinations" help="(-x)"/>
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141 <param name="max_rounds" type="integer" optional="true" value="50" label="Perform N rounds of consensus sequence improvement" help="(--max_rounds)"/>
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142 <param name="ploidy" type="integer" optional="true" value="-1" label="The ploidy level of the sequenced genome. -1:disabled" help="(-p)"/>
1
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143 <param name="min_flanking_sequence" type="integer" optional="true" value="" label="Distance from alignment end to calculate variants" help="(--min-flanking-sequence)"/>
0
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144
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145 <!-- optional flags -->
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146 <param argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" checked="true" label="Consensus calling mode and output polished sequence" />
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147 <param argument="--snps" type="boolean" truevalue="--snps" falsevalue="" checked="false" label="only call SNPs"/>
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148 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="verbose output"/>
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149 <param name="homopolymer" type="boolean" argument="--fix-homopolymers" truevalue="--fix-homopolymers" falsevalue="" checked="false" label="homopolymer caller" />
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150 <param argument="--faster" type="boolean" truevalue="--faster" falsevalue="" checked="false"
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151 label="speedup while slightly reducing consensus accuracy"/>
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152 <param name="all_bases" type="boolean" argument="--calculate-all-support" truevalue="--calculate-all-support" falsevalue="" checked="false"
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153 label="calculate the support of the 3 other possible bases" />
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154 </inputs>
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155
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156 <outputs>
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157 <!-- variants consensus outputs -->
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158 <data name="output_polished" format="fasta" from_work_dir="polished.fa" label="polished sequence by consensus calling mode" />
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159 <data name="output_variants" format="vcf" from_work_dir="variants.vcf" label="Computed variants"/>
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160 </outputs>
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161 <tests>
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162 <test>
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163 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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164 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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165 <param name="b" value="reads.sorted.bam" />
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166 <param name="reference_source_selector" value="history" />
3
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167 <param name="ref_file" value="draft_single_seq.fa" />
0
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168 <param name="w" value="tig00000001:200000-202000" />
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169 <output name="output_polished" file="polished.fa" />
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170 <output name="output_variants" file="variants.vcf"/>
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171 </test>
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172 <test>
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173 <param name="input_merged" ftype="fasta" value="reads.fasta" />
3
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174 <param name="input_reads_raw" ftype="fast5.tar.bz2" value="fast5_files.tar.bz2" />
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175 <param name="b" value="reads.sorted.bam" />
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176 <param name="reference_source_selector" value="history" />
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177 <param name="ref_file" value="draft_single_seq.fa" />
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178 <param name="w" value="tig00000001:200000-202000" />
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179 <output name="output_polished" file="t3_polished.fa" />
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180 <output name="output_variants" file="t3_variants.vcf"/>
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181 </test>
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182 <test>
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183 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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184 <param name="input_reads_raw" ftype="fast5.tar" value="fast5_files.tar" />
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185 <param name="b" value="reads.sorted.bam" />
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186 <param name="reference_source_selector" value="history" />
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187 <param name="ref_file" value="draft_single_seq.fa" />
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188 <param name="w" value="tig00000001:200000-202000" />
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189 <output name="output_polished" file="t4_polished.fa" />
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190 <output name="output_variants" file="t4_variants.vcf"/>
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191 </test>
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192 <test>
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193 <param name="input_merged" ftype="fasta" value="reads.fasta" />
0
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194 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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195 <param name="b" value="reads.sorted.bam" />
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196 <param name="reference_source_selector" value="history" />
3
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197 <param name="ref_file" value="draft_single_seq.fa" />
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198 <param name="w" value="tig00000001:198000-202000" />
0
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199 <param name="ploidy" value="2" />
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200 <param name="snps" value="true" />
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201 <param name="faster" value="true" />
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202 <param name="all_bases" value="true" />
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203 <param name="consensus" value="false" />
3
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204 <param name="min_flanking_sequence" value="10" />
0
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205 <output name="output_polished" file="t2-polished.fa" />
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206 <output name="output_variants" file="t2-variants.vcf"/>
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207 </test>
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208 </tests>
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209 <help><![CDATA[
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210
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211 Build an index mapping from basecalled reads to the signals measured by the sequencer
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212 and
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213 Find SNPs using a signal-level HMM
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214
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215 Tutorial and manual available at:
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216 http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html
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217
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218
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219 ]]></help>
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220 <expand macro="citations" />
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221 </tool>