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annotate biohansel.xml @ 10:cd6682c83b22 draft default tip

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"planemo upload for repository https://github.com/phac-nml/biohansel commit 4fdee1b82288e821ab2cf60d9476c3b83775f337"
author nml
date Mon, 21 Oct 2019 09:32:21 -0400
parents e305df0b1af7
children
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cd6682c83b22 "planemo upload for repository https://github.com/phac-nml/biohansel commit 4fdee1b82288e821ab2cf60d9476c3b83775f337"
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1 <tool id="biohansel" name="biohansel" version="2.4.0">
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2 <description>SNP subtyping of genome sequence reads or assemblies</description>
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3 <requirements>
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4 <requirement type="package" version="2.4.0">bio_hansel</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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9 #import re
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10 #import os
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12 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38)
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13 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$')
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14 #set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)')
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16 #def is_gzipped_fastq($data_input)
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17 ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
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18 #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz')
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19 #end def
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21 #def get_fastq_ext($data_input)
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22 ## Get file extension for FASTQ data param
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23 #return '.fastq.gz' if $is_gzipped_fastq($data_input) else '.fastq'
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24 #end def
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26 #def base_sample_name($name)
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27 ## Get the base sample name and append 1/2 depending on if forward/reverse read
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28 #set $illumina_match = $ILLUMINA_REGEX.match($name)
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29 #set $fastq_dump_match = $FASTQ_DUMP_REGEX.match($name)
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30
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31 #if $illumina_match
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32 #return $illumina_match.group(1)
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33 #elif $fastq_dump_match
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34 #return $fastq_dump_match.group(1)
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35 #elif $re.search(r'_R(1|2)', $name):
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36 #return $re.sub(r'(.+)_R(1|2)([^\.]*)(\..+)', r'\1\3', $name)
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37 #elif $re.match(r'.+_\d\.', $name):
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38 #return $re.sub(r'(.+)_(\d)(\..+)', r'\1', $name)
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39 #else
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40 #return $name
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41 #end if
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42 #end def
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43
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44 #def get_paired_fastq_filename($data_input, $name=None, $is_forward=True)
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45 ## Get paired FASTQ filename for a data param with appropriate file extension
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46 ## with '_1' or '_2' appended if forward or reverse reads, respectively.
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47 #set $name = $name if $name is not None else $data_input.name
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48 #set $name = $base_sample_name($name)
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49 #set $postfix = '1' if $is_forward else '2'
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50 #set $ending = '_{}{}'.format($postfix, $get_fastq_ext($data_input))
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51 #return '"{}"'.format($name) if $ending in $name else '"{}{}"'.format($name, $ending)
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52 #end def
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54 ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz)
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55 #if $input.type == 'fasta'
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56 #set $input_files = '"{}.fasta"'.format(os.path.splitext($input.fasta.name)[0])
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57 ln -s "$input.fasta" $input_files &&
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58 #elif $input.type == 'paired'
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59 #set $forward_filename = $get_paired_fastq_filename($input.forward)
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60 #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False)
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61 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
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62 ln -s "$input.forward" $forward_filename &&
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63 ln -s "$input.reverse" $reverse_filename &&
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64 #elif $input.type == 'single'
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65 #set $input_files = '"{}"'.format($input.single.name)
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66 ln -s "$input.single" $input_files &&
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67 #elif $input.type == 'paired_collection'
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68 #set $forward_filename = $get_paired_fastq_filename($input.paired_collection.forward)
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69 #set $reverse_filename = $get_paired_fastq_filename($input.paired_collection.reverse, is_forward=False)
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70 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
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71 ln -s "$input.paired_collection.forward" $forward_filename &&
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72 ln -s "$input.paired_collection.reverse" $reverse_filename &&
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73 #end if
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75 ## Checking for custom scheme.
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76 #if $type_of_scheme.scheme_check == "custom":
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77 #if $type_of_scheme.scheme_input.is_of_type('fasta'):
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78 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' &&
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79 #end if
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80 #end if
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81
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82 #def get_subtype_metadata_filename($data_input)
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83 ## Ensure that the subtype metadata table file has the proper extension - .tab or .csv
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84 #set $filename = $data_input.name
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85 #if $data_input.is_of_type('tabular')
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86 #return '{}.tab'.format($filename)
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87 #elif $data_input.is_of_type('csv')
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88 #return '{}.csv'.format($filename)
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89 #else
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90 #return None
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91 #end if
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92 #end def
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93
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94 ## Symlink to subtype metadata table if it is specified
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95 #if $subtype_metadata
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96 #set global $subtype_metadata_filename = $get_subtype_metadata_filename($subtype_metadata)
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97 #if $subtype_metadata_filename
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98 ln -s '$subtype_metadata' '$subtype_metadata_filename' &&
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99 #end if
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100 #else
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101 #set global $subtype_metadata_filename = None
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102 #end if
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103
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104 #################################
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105 ## biohansel command starts here:
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106 #################################
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107 hansel
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108 -vvv
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109 -t "\${GALAXY_SLOTS:-1}"
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110 -o results.tab
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111 -O match_results.tab
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112 -S tech_results.tab
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113 $dev_args.use_json
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114 $input_files
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115 --scheme
7
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116 #if $type_of_scheme.scheme_check == "custom":
0
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117 '$type_of_scheme.scheme_input.name'
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118 #else:
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119 $type_of_scheme.scheme_type
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120 #end if
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121 #if $subtype_metadata_filename
4
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122 --scheme-metadata '$subtype_metadata_filename'
0
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123 #end if
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124 #if $kmer_vals.kmer_min
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125 --min-kmer-freq $kmer_vals.kmer_min
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126 #end if
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127 #if $kmer_vals.kmer_max
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128 --max-kmer-freq $kmer_vals.kmer_max
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129 #end if
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130 #if $qc_vals.low_cov_depth_freq
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131 --low-cov-depth-freq $qc_vals.low_cov_depth_freq
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132 #end if
8
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133 #if $qc_vals.max_missing_kmers
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134 --max-missing-kmers $qc_vals.max_missing_kmers
0
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135 #end if
8
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136 #if $qc_vals.min_ambiguous_kmers
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137 --min-ambiguous-kmers $qc_vals.min_ambiguous_kmers
0
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138 #end if
8
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139 #if $qc_vals.max_intermediate_kmers
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140 --max-intermediate-kmers $qc_vals.max_intermediate_kmers
0
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141 #end if
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142 #if $qc_vals.low_coverage_warning
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143 --low-cov-warning $qc_vals.low_coverage_warning
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144 #end if
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145 ]]>
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146 </command>
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147 <inputs>
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148 <conditional name="input">
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149 <param name="type" type="select" label="Sequence Data Type">
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150 <option value="fasta">Contigs (FASTA)</option>
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151 <option value="paired">Paired-end reads (FASTQ)</option>
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152 <option value="single">Single-end reads (FASTQ)</option>
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153 <option value="paired_collection">Paired-end reads collection (FASTQ)</option>
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154 </param>
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155 <when value="fasta">
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156 <param name="fasta"
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157 type="data" format="fasta"
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158 optional="false"
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159 label="Contigs (FASTA)"
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160 />
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161 </when>
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162 <when value="paired">
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163 <param name="forward"
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164 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
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165 optional="false"
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166 label="Forward reads (FASTQ)"
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167 help="Must have ASCII encoded quality scores"
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168 />
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169 <param name="reverse"
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170 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
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171 optional="false"
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172 label="Reverse reads (FASTQ)"
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173 help="File format must match the Forward FASTQ file"
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174 />
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175 </when>
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176 <when value="single">
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177 <param name="single"
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178 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
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179 optional="false"
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180 label="Single-end reads (FASTQ)"
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181 />
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182 </when>
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183 <when value="paired_collection">
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184 <param name="paired_collection"
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185 type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,txt"
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186 collection_type="paired"
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187 optional="false"
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188 label="Paired-end reads collection (FASTQ)"
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189 />
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190 </when>
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191 </conditional>
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192 <conditional name="type_of_scheme">
7
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193 <param name="scheme_check" type="select"
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194 label="Subtyping Schemes"
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195 help="Use included scheme or custom">
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196 <option value="standard">Included Biohansel Schemes</option>
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197 <option value="custom">Select User Custom Scheme</option>
0
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198 </param>
7
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199 <when value="standard">
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200 <param name="scheme_type" type="select"
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201 label="Included SNP Subtyping Scheme">
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202 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
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203 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
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204 <option value="typhi">Salmonella Typhi subtyping scheme</option>
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205 <option value="typhimurium">Salmonella Typhimurium subtyping scheme</option>
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206 <option value="tb_lineage">Mycobacterium Tuberculosis subtyping scheme</option>
7
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207 </param>
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208 </when>
0
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209 <when value="custom">
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210 <param name="scheme_input"
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211 type="data" format="fasta"
7
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212 label="Your Custom Biohansel SNP Subtyping Scheme"/>
0
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213 </when>
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214 </conditional>
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215 <param name="subtype_metadata"
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216 type="data" format="tabular"
0
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217 optional="true"
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218 label="Scheme Subtype Metadata Table (tsv) [Optional]"
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219 help="Tab-delimited format only (.tsv) to add metadata table to results. Must contain a column called 'subtype'."
0
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220 />
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221 <!-- K-mer frequencies. -->
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222 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
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223 <param name="kmer_min" type="integer"
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224 argument="--min-kmer-freq"
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225 optional="true"
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226 min="0" value="8"
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227 label="Min k-mer frequency/coverage"
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228 help="default = 8"/>
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229 <param name="kmer_max" type="integer"
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230 argument="--max-kmer-freq"
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231 optional="true"
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232 min="1" value="1000"
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233 label="Max k-mer frequency/coverage"
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234 help="default = 1000"/>
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235 </section>
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236 <!-- Quality Checking Parameters -->
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237 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
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238 <param name="low_cov_depth_freq" type="integer"
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239 argument="--low-cov-depth-freq"
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240 value="20" min="0"
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241 optional="true"
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242 label="QC: Frequency below this coverage are considered low coverage"
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243 help="default = 20"/>
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244 <param name="min_ambiguous_kmers" type="integer"
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245 argument="--min-ambiguous-kmers"
0
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246 optional="true"
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247 value="3" min="0"
8
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248 label="QC: Min number of kmers missing for Ambiguous Result"
0
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249 help="default = 3"/>
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250 <param name="max_missing_kmers" type="float"
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251 argument="--max-missing-kmers"
0
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252 optional="true"
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253 value="0.05" min="0" max="1"
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254 label="QC: Decimal Proportion of max allowed missing kmers" help="default = 0.05, valid values {0.0 - 1.0}"/>
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255 <param name="max_intermediate_kmers" type="float"
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256 argument="--max-intermediate-kmers"
0
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257 optional="true"
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258 value="0.05" min="0" max="1"
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259 label="QC: Decimal Proportion of max allowed missing kmers for an intermediate subtype"
0
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260 help="default = 0.05, valid values {0.0 - 1.0}"/>
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261 <param name="low_coverage_warning" type="integer"
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262 argument="--low-cov-warning"
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263 optional="true"
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264 value="20"
8
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265 label="QC: Overall kmer coverage below this value will trigger a low coverage warning"
0
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266 help="default = 20"/>
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267 </section>
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268 <section name="dev_args" title="Developer Options" expanded="False">
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269 <param name="use_json"
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270 type="boolean"
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271 checked="false"
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272 truevalue="--json"
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273 falsevalue=""
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274 label="Output JSON results"
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275 help="Use this option of you need json representations of analysis' details"/>
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276 </section>
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277 </inputs>
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278 <outputs>
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279 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
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280 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
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281 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
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282 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
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283 <filter>dev_args['use_json']</filter>
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284 </data>
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285 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
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286 <filter>dev_args['use_json']</filter>
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287 </data>
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288 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
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289 <filter>dev_args['use_json']</filter>
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290 </data>
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291 </outputs>
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292 <tests>
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293 <test>
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294 <conditional name="input">
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295 <param name="type" value="fasta"/>
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296 <param name="fasta" value="SRR1002850_SMALL.fasta"/>
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297 </conditional>
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298 <param name="type_of_scheme" value="heidelberg"/>
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299 <output name="results.tab"
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300 value="SRR1002850_SMALL.fasta-results.tab"
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301 ftype="tabular"
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302 compare="sim_size"
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303 delta="1000">
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304 </output>
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305 <output name="match_results.tab"
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306 value="SRR1002850_SMALL.fasta-match_results.tab"
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307 ftype="tabular"
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308 compare="sim_size"
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309 delta="16000">
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310 </output>
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311 <output name="tech_results.tab"
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312 value="SRR1002850_SMALL.fasta-tech_results.tab"
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313 ftype="tabular"
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314 lines_diff="0">
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315 </output>
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316 </test>
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317 <test>
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318 <conditional name="input">
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319 <param name="type" value="paired"/>
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320 <param name="forward" value="SRR5646583_SMALL_1.fastq"/>
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321 <param name="reverse" value="SRR5646583_SMALL_2.fastq"/>
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322 </conditional>
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323 <param name="type_of_scheme" value="heidelberg"/>
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324 <output name="tech_results.tab"
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325 value="SRR5646583_SMALL-tech_results.tab"
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326 ftype="tabular"
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327 lines_diff="0">
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328 </output>
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329 <output name="results.tab"
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330 value="SRR5646583_SMALL-results.tab"
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331 ftype="tabular"
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332 compare="sim_size"
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333 delta="1000">
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334 </output>
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335 <output name="match_results.tab"
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336 value="SRR5646583_SMALL-match_results.tab"
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337 ftype="tabular"
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338 compare="sim_size"
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339 delta="16000">
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340 </output>
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341 </test>
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342 </tests>
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343 <help><![CDATA[
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344 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes.
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345
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346 **Usage**
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347
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348 1) Select the sequence data you wish to subtype (FASTAs or FASTQs)
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349 2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg, Enteritidis, Typhimurium, or Typhi subtyping scheme, or your own custom `biohansel` compatible subtyping scheme)
0
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350 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results
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351 4) Click ``Execute``
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352
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353 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_ or the `biohansel read the docs page <https://bio-hansel.readthedocs.io/en/readthedocs/>`_.
0
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354
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355
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356 **Example analysis results of a single FASTA file**
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357
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358 Contents of ``results.tab``:
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359
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360 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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361 | sample | scheme | scheme_version | subtype | all_subtypes | kmers_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_kmers_matching_all | n_kmers_matching_all_expected | n_kmers_matching_positive | n_kmers_matching_positive_expected | n_kmers_matching_subtype | n_kmers_matching_subtype_expected | file_path | qc_status | qc_message |
0
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362 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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363 | SRR1002850_SMALL | heidelberg | 0.5.0 | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | SRR1002850_SMALL.fasta | PASS | |
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364 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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365
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366
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367 Contents of ``match_results.tab``:
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368
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369 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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370 | kmername | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_kmer | sample | file_path | scheme | scheme_version | qc_status | qc_message |
0
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371 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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372 | 2154958-2.2.2.2.1.4 | GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG | True | NODE_1_length_726282_cov_40.4705_ID_1 | 13732 | 2154958 | 2.2.2.2.1.4 | True | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
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373 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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374 | negative2131791-2.2.3.1.3 | GCTGGGCGAAATGATGCAGTTCACCACTTGCTC | True | NODE_1_length_726282_cov_40.4705_ID_1 | 36900 | 2131791 | 2.2.3.1.3 | False | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
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375 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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376
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377 *Next 201 lines omitted.*
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378
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379
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380
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381 **Example analysis results of a single FASTQ readset**
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382
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383
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384 Contents of ``results.tab``:
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385
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386 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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387 | sample | scheme | scheme_version | subtype | all_subtypes | kmers_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_kmers_matching_all | n_kmers_matching_all_expected | n_kmers_matching_positive | n_kmers_matching_positive_expected | n_kmers_matching_subtype | n_kmers_matching_subtype_expected | file_path | avg_kmer_coverage | qc_status | qc_message |
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388 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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389 | SRR5646583_SMALL | heidelberg | 0.5.0 | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] | 42.631 | PASS | |
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390 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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391
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392 Contents of ``match_results.tab``:
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393
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394 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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395 | kmername | seq | freq | refposition | subtype | is_pos_kmer | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |
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396 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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397 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
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398 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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399 | 21097-2.2.1.1.1 | GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT | 42 | 21097 | 2.2.1.1.1 | True | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
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400 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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401
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402 *Next 202 lines omitted.*
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403
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404
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405 **Example Subtype Metadata**
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406
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407 A column with name `subtype` must exist and should have subtype designations that would appear in your biohansel results. There are no requirements for the number of columns or contents of those columns in the table - they can contain whatever you want.
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408 Metadata must be structured in a tab-delimited format (.tsv) to be a valid input.
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409
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410 +-------------+-------+--------+------------------+
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411 | subtype | clade | source | disease_symptoms |
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412 +-------------+-------+--------+------------------+
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413 | 1 | I | geese | death |
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414 +-------------+-------+--------+------------------+
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415 | 1.1 | I | moose | burns |
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416 +-------------+-------+--------+------------------+
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417 | 2.2.1.1.1 | II | mouse | boils |
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418 +-------------+-------+--------+------------------+
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419 | 2.2.2.2.1.4 | IIa | house | rash |
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420 +-------------+-------+--------+------------------+
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421
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422 The `biohansel` results table will be joined with the subtype metadata table on the `subtype` field so if there are subtype metadata for your `biohansel` results, it will show up in the final output table. For example, if you have a sample that produces a result with subtype "1", there will also be columns "clade", "source" and "disease_symptoms" with "I", "geese" and "death", respectively.
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423
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424
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425 Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory.
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426
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427 ]]></help>
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428 <citations>
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429 <citation type="bibtex">@ARTICLE{a1,
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430 title = {Rapid and robust genotyping of highly clonal bacterial pathogens using BioHansel, a SNP-based k-mer search pipeline},
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431 author = {Geneviève Labbé, Peter Kruczkiewicz, Philip Mabon, James Robertson, Justin Schonfeld, Daniel Kein, Marisa A. Rankin, Matthew Gopez, Darian Hole, David Son, Natalie Knox, Chad R. Laing, Kyrylo Bessonov, Eduardo Taboada, Catherine Yoshida, Anil Nichani, Roger P. Johnson, Gary Van Domselaar, John H.E. Nash},
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432 url = {https://github.com/phac-nml/biohansel}
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433 }
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434 }</citation>
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435 </citations>
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436 </tool>