annotate bio_hansel.xml @ 7:af59ac462926 draft

planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4fee4519135f7677cf50f721cf1ad7a7335ad66d-dirty
author nml
date Fri, 06 Apr 2018 14:20:32 -0400
parents 5a42e475436e
children e9fd173fc7ee
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1 <tool id="bio_hansel" name="Bio Hansel" version="1.3.0">
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2 <description>SNV Subtyping with genome assemblies or reads</description>
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3 <requirements>
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4 <requirement type="package" version="1.3.0">bio_hansel</requirement>
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5 <requirement type="package" version="17.2.0">attrs</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 ## Preparing file input.
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9 #if $data_type.type == "paired":
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5
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11 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq &&
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12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name'.fastq &&
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14 #elif $data_type.type == "collection":
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16 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
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17 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&
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19 #elif $data_type.type == "single":
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1
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21 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
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22 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq &&
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23 #end if
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25 #if $data_type.fastq_input1.is_of_type('fasta'):
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26 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fasta &&
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27 #end if
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29 #end if
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32 ## Checking for custom scheme.
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33 #if $type_of_scheme.scheme_type == "custom":
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34 #if $type_of_scheme.scheme_input.is_of_type('fasta'):
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35 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' &&
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36 #end if
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37 #end if
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39 ## Start the actual command here
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40 hansel
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43 ## Select the scheme
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44 -s
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46 #if $type_of_scheme.scheme_type == "heidelberg":
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47 heidelberg
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48 #elif $type_of_scheme.scheme_type == "enteritidis":
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49 enteritidis
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50 #elif $type_of_scheme.scheme_type == "custom":
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51 '$type_of_scheme.scheme_input.name'
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52 #end if
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53
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54 ## Use Json output
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55 #if $dev_args.use_json == "yes":
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56 --json
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57 #end if
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58
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59 #if $kmer_vals.kmer_min
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60 --min-kmer-freq $kmer_vals.kmer_min
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61 #end if
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63 #if $kmer_vals.kmer_max
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64 --max-kmer-freq $kmer_vals.kmer_max
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65 #end if
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66
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67 #if $qc_vals.low_cov_depth_freq
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68 --low-cov-depth-freq $qc_vals.low_cov_depth_freq
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69 #end if
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71 #if $qc_vals.max_missing_tiles
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72 --max-missing-tiles $qc_vals.max_missing_tiles
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73 #end if
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75 #if $qc_vals.min_ambiguous_tiles
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76 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles
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77 #end if
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79 #if $qc_vals.max_intermediate_tiles
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80 --max-intermediate-tiles $qc_vals.max_intermediate_tiles
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81 #end if
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82
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83 #if $qc_vals.low_coverage_warning
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84 --low-cov-warning $qc_vals.low_coverage_warning
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85 #end if
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86
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87 ## Adding more parameters to the command.
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88 -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab
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90
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91 ## Entering the file inputs
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92
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93 #if $data_type.type == "single":
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95 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
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96 '$data_type.fastq_input1.name'.fastq
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97 #end if
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98
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99 #if $data_type.fastq_input1.is_of_type('fasta'):
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100 '$data_type.fastq_input1.name'.fasta
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101 #end if
0
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102
1
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103 #elif $data_type.type =="collection":
5
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104 -p '$data_type.fastq_input1.name'_1.fastq '$data_type.fastq_input1.name'_2.fastq
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105
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106 #elif $data_type.type =="paired":
5
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107 -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq
0
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108 #end if
1
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109
0
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110 ]]></command>
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111 <inputs>
1
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112 <conditional name="data_type">
0
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113 <param name="type" type="select" label="Specify the read type.">
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114 <option value="single">Single-end Data</option>
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115 <option value="paired">Paired-end Data</option>
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116 <option value="collection">Collection Paired-end Data</option>
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117 </param>
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118 <when value="single">
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119 <param name="fastq_input1" type="data" format="fastqsanger, fastq, fasta" label="Single end read file(s)"/>
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120 </when>
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121 <when value="paired">
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122 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
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123 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
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124 </when>
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125 <when value="collection">
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126 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
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127 </when>
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128 </conditional>
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129 <conditional name="type_of_scheme">
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130 <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)">
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131 <option value="heidelberg">Heidelberg scheme</option>
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132 <option value="enteritidis">Enteritidis scheme</option>
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133 <option value="custom">Specify your own custom scheme</option>
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134 </param>
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135 <when value="heidelberg"/>
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136 <when value="enteritidis"/>
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137 <when value="custom">
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138 <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/>
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139 </when>
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140 </conditional>
3
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141 <!-- K-mer frequencies. -->
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142 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
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143 <param name="kmer_min" argument="--min-kmer-freq" optional="True" type="integer" min="0" label="Min k-mer freq/coverage" value="8" help="default = 8"/>
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144 <param name="kmer_max" argument="--max-kmer-freq" optional="True" type="integer" min="1" label="Max k-mer freq/coverage" value="1000" help="default = 1000"/>
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145 </section>
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146 <!-- Quality Checking Parameters -->
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147 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
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148 <param name="low_cov_depth_freq" argument="--low-cov-depth-freq" optional="True" type="integer" min="0" label="QC: Frequency below this coverage are considered low coverage" value="20" help="default = 20"/>
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149 <param name="min_ambiguous_tiles" argument="--min-ambiguous-tiles" optional="True" type="integer" min="0" label="QC: Min number of tiles missing for Ambiguous Result" value="3" help="default = 3"/>
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150 <param name="max_missing_tiles" argument="--max-missing-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/>
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151 <param name="max_intermediate_tiles" argument="--max-intermediate-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/>
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152 <param name="low_coverage_warning" argument="--low-cov-warning" optional="True" type="integer" min="0" label="QC: Overall tile coverage below this value will trigger a low coverage warning" value="20" help="default = 20"/>
3
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153 </section>
5
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154 <section name="dev_args" title="Developer Options" expanded="False">
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155 <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details">
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156 <option value="no">no</option>
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157 <option value="yes">yes</option>
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158 </param>
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159 </section>
0
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160 </inputs>
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161 <outputs>
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162 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
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163 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
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164 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
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165 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
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166 <filter>dev_args['use_json'] == "yes"</filter>
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167 </data>
5
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168 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
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169 <filter>dev_args['use_json'] == "yes"</filter>
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170 </data>
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171 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
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172 <filter>dev_args['use_json'] == "yes"</filter>
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173 </data>
0
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174 </outputs>
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175 <tests>
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176 <test>
1
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177 <param name="type" value="single"/>
0
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178 <param name="type_of_scheme" value="heidelberg"/>
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179 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
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180 <output name="results.tab">
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181 <assert_contents>
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182 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/>
0
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183 </assert_contents>
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184 </output>
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185 <output name="match_results.tab">
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186 <assert_contents>
3
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187 <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>
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188 </assert_contents>
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189 </output>
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190 <output name="tech_results.tab">
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191 <assert_contents>
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192 <has_text_matching expression="sample\s+subtype\s+qc_status\s+qc_message"/>
0
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193 </assert_contents>
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194 </output>
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195 </test>
1
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196 <test>
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197 <param name="type" value="paired"/>
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198 <param name="type_of_scheme" value="heidelberg"/>
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199 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>
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200 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
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201 <output name="results.tab">
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202 <assert_contents>
7
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203 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+avg_tile_coverage\s+qc_status\s+qc_message"/>
3
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204 </assert_contents>
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205 </output>
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206 <output name="match_results.tab">
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207 <assert_contents>
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208 <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>
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209 </assert_contents>
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210 </output>
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211 <output name="tech_results.tab">
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212 <assert_contents>
5
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213 <has_text_matching expression="sample\s+subtype\s+avg_tile_coverage\s+qc_status\s+qc_message"/>
1
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214 </assert_contents>
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215 </output>
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216 </test>
0
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217 </tests>
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218 <help><![CDATA[
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219 ***********************************************************
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220 bio_hansel - Heidelberg And eNteritidis Snp ELucidation
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221 ***********************************************************
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222
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223 Subtype *Salmonella enterica* subsp. enterica serovar Heidelberg and Enteritidis genomes using *in-silico* 33 bp k-mer SNP subtyping schemes developed by Genevieve Labbe et al.
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224 Subtype *Salmonella* genome assemblies (FASTA files) and/or whole-genome sequencing reads (FASTQ files)!
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225
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226 Usage
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227 =====
1
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228 1) Enter your FASTA/FASTQ file(s)
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229 2) Select which scheme you would like to use (e.g. heidelberg, enteritidis, or specify your own)
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230 3) Click Execute
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231
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232 For more information visit `https://github.com/phac-nml/bio_hansel`
0
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233
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234
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235 Example Usage
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236 =============
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237
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238 Analysis of a single FASTA file
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239 -------------------------------
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240
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241
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242 Contents of ``results.tab``:
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243
1
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244 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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245 | sample | scheme | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_total | n_tiles_matching_positive | n_tiles_matching_positive_total | n_tiles_matching_subtype | n_tiles_matching_subtype_total | file_path |
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246 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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247 | file.fasta | heidelberg | 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 | 1037658-2.2.2.2.1.4; 2154958-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | file.fasta |
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248 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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249
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250
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251
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252 Contents of ``match_results.tab``:
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253
1
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254 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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255 | tilename | stitle | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | qlen | slen | seq | coverage | is_trunc | refposition | subtype | is_pos_tile | sample | file_path | scheme |
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256 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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257 | 775920-2.2.2.2 | NODE_2_length_512016_cov_46.4737_ID_3 | 100 | 33 | 0 | 0 | 1 | 33 | 474875 | 474907 | 2E-11 | 62.1 | 33 | 512016 | GTTCAGGTGCTACCGAGGATCGTTTTTGGTGCG | 1 | False | 775920 | 2.2.2.2 | True | out | file.fasta | heidelberg |
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258 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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259 | negative3305400-2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 276235 | 276267 | 2E-11 | 62.1 | 33 | 427905 | CATCGTGAAGCAGAACAGACGCGCATTCTTGCT | 1 | False | negative3305400 | 2.1.1.1 | False | out | file.fasta | heidelberg |
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260 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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261 | negative3200083-2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 170918 | 170950 | 2E-11 | 62.1 | 33 | 427905 | ACCCGGTCTACCGCAAAATGGAAAGCGATATGC | 1 | False | negative3200083 | 2.1 | False | out | file.fasta | heidelberg |
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262 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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263 | negative3204925-2.2.3.1.5 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 175760 | 175792 | 2E-11 | 62.1 | 33 | 427905 | CTCGCTGGCAAGCAGTGCGGGTACTATCGGCGG | 1 | False | negative3204925 | 2.2.3.1.5 | False | out | file.fasta | heidelberg |
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264 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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265 | negative3230678-2.2.2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 201513 | 201545 | 2E-11 | 62.1 | 33 | 427905 | AGCGGTGCGCCAAACCACCCGGAATGATGAGTG | 1 | False | negative3230678 | 2.2.2.1.1.1 | False | out | file.fasta | heidelberg |
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266 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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267 | negative3233869-2.1.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 204704 | 204736 | 2E-11 | 62.1 | 33 | 427905 | CAGCGCTGGTATGTGGCTGCACCATCGTCATTA | 1 | False | negative3233869 | 2.1.1.1.1 | False | out | file.fasta | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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268 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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269 | negative3254229-2.2.3.1.3 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 225064 | 225096 | 2E-11 | 62.1 | 33 | 427905 | CGCCACCACGCGGTTAGCGTCACGCTGACATTC | 1 | False | negative3254229 | 2.2.3.1.3 | False | out | file.fasta | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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270 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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271 | negative3257074-2.2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 227909 | 227941 | 2E-11 | 62.1 | 33 | 427905 | CGGCAACCAGACCGACTACGCCGCCAAGCAGAC | 1 | False | negative3257074 | 2.2.1 | False | out | file.fasta | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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272 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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273 | negative3264474-2.2.2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 235309 | 235341 | 2E-11 | 62.1 | 33 | 427905 | AATGGCGCCGATCGTCGCCAGATAACCGTTGCC | 1 | False | negative3264474 | 2.2.2.1.1.1 | False | out | file.fasta | heidelberg |
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274 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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275 | negative3267927-2.2.2.2.2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 238762 | 238794 | 2E-11 | 62.1 | 33 | 427905 | AAAGAGAAATATGATGCCAGGCTGATACATGAC | 1 | False | negative3267927 | 2.2.2.2.2.1 | False | out | file.fasta | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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276 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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277 | negative3278067-1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 248902 | 248934 | 2E-11 | 62.1 | 33 | 427905 | TGTGAGTAAGTTGCGCGATATTCTGCTGGATTC | 1 | False | negative3278067 | 1.1 | False | out | file.fasta | heidelberg |
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278 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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279 | negative3299717-2.2.3.1.4 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 270552 | 270584 | 2E-11 | 62.1 | 33 | 427905 | ATGCCGGACAGCAGGCGAAACTCGAACCGGATA | 1 | False | negative3299717 | 2.2.3.1.4 | False | out | file.fasta | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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280 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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281 | negative3373069-2.2.2.2.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 344011 | 344043 | 2E-11 | 62.1 | 33 | 427905 | CTCTCCAGAAGATGAAGCCCGTGATGCGGCGCA | 1 | False | negative3373069 | 2.2.2.2.1.1 | False | out | file.fasta | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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282 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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283
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284 Next 196 lines omitted.
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285
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287
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288 Analysis of a single FASTQ readset
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289 ----------------------------------
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290
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291 Contents of ``results.tab``:
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292
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293 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
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294 | sample | scheme | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_total | n_tiles_matching_positive | n_tiles_matching_positive_total | n_tiles_matching_subtype | n_tiles_matching_subtype_total | file_path |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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295 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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296 | 564 | heidelberg | 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 | forward.fastqsanger; reverse.fastqsanger |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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297 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
0
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300 Contents of ``match_results.tab``:
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301
1
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302 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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303 | seq | freq | sample | file_path | tilename | is_pos_tile | subtype | refposition | is_kmer_freq_okay | scheme |
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304 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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305 | ACGGTAAAAGAGGACTTGACTGGCGCGATTTGC | 68 | 564 | forward.fastqsanger; reverse.fastqsanger | 21097-2.2.1.1.1 | True | 2.2.1.1.1 | 21097 | True | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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306 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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307 | AACCGGCGGTATTGGCTGCGGTAAAAGTACCGT | 77 | 564 | forward.fastqsanger; reverse.fastqsanger | 157792-2.2.1.1.1 | True | 2.2.1.1.1 | 157792 | True | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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308 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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309 | CCGCTGCTTTCTGAAATCGCGCGTCGTTTCAAC | 67 | 564 | forward.fastqsanger; reverse.fastqsanger | 293728-2.2.1.1 | True | 2.2.1.1 | 293728 | True | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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310 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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311 | GAATAACAGCAAAGTGATCATGATGCCGCTGGA | 91 | 564 | forward.fastqsanger; reverse.fastqsanger | 607438-2.2.1 | True | 2.2.1 | 607438 | True | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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312 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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313 | CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA | 87 | 564 | forward.fastqsanger; reverse.fastqsanger | 691203-2.2.1.1 | True | 2.2.1.1 | 691203 | True | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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314 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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315 | CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC | 33 | 564 | forward.fastqsanger; reverse.fastqsanger | 944885-2.2.1.1.1 | True | 2.2.1.1.1 | 944885 | True | heidelberg |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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316 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
0
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317
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318 Next 200 lines omitted.
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319
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320 Galaxy wrapper written by Matthew Gopez at the Public Health Agency of Canada, National Microbiology Laboratory.
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321
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322 ]]></help>
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323 <citations>
1
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324 <citation type="bibtex">@ARTICLE{a1,
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325 title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},
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326 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},
1
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327 url = {https://github.com/phac-nml/bio_hansel}
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328 }
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329 }</citation>
0
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330 </citations>
6
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331 </tool>