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annotate bio_hansel.xml @ 4:c0d08ba0c6ee draft

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planemo upload for repository https://github.com/phac-nml/bio_hansel commit 08fbb2e77de0baf6b84c0ca025456f027b1e52a6-dirty
author nml
date Fri, 26 Jan 2018 11:27:16 -0500
parents 29faaa849e41
children 6396d043667b
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c0d08ba0c6ee planemo upload for repository https://github.com/phac-nml/bio_hansel commit 08fbb2e77de0baf6b84c0ca025456f027b1e52a6-dirty
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1 <tool id="bio_hansel" name="Bio Hansel" version="1.0.1">
3
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2 <description>SNV Subtyping with genome assemblies or reads</description>
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3 <requirements>
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c0d08ba0c6ee planemo upload for repository https://github.com/phac-nml/bio_hansel commit 08fbb2e77de0baf6b84c0ca025456f027b1e52a6-dirty
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4 <requirement type="package" version="1.1.3">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[
1
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8 ## Preparing file input.
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9 #if $data_type.type == "paired":
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1
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11 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' &&
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12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name' &&
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14 #elif $data_type.type == "collection":
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2
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16 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1 &&
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17 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2 &&
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1
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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' &&
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23 #end if
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1
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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' &&
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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 $type_of_scheme.scheme_input.is_of_type('fasta'):
1
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35 ln -s '$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 $type_of_scheme.scheme_type == "custom":
1
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51 '$type_of_scheme.scheme_input.name'
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52 #end if
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54
3
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55 #if $kmer_vals.kmer_min
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56 --min-kmer-freq $kmer_vals.kmer_min
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57 #end if
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59 #if $kmer_vals.kmer_max
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60 --max-kmer-freq $kmer_vals.kmer_max
0
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61 #end if
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62
3
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63 #if $qc_vals.low_cov_depth_freq
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64 --low-cov-depth-freq $qc_vals.low_cov_depth_freq
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65 #end if
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66
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67 #if $qc_vals.max_missing_tiles
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68 --max-missing-tiles $qc_vals.max_missing_tiles
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69 #end if
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70
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71 #if $qc_vals.min_ambiguous_tiles
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72 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles
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73 #end if
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75 #if $qc_vals.max_intermediate_tiles
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76 --max-intermediate-tiles $qc_vals.max_intermediate_tiles
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77 #end if
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79 ## Adding more parameters to the command.
3
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80 -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab
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82
1
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83 ## Entering the file inputs
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84
1
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85 #if $data_type.type == "single":
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86 '$data_type.fastq_input1.name'
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87
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88 #elif $data_type.type =="collection":
2
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89 -p '$data_type.fastq_input1.name'_1 '$data_type.fastq_input1.name'_2
1
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91 #elif $data_type.type =="paired":
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92 -p '$data_type.fastq_input1.name' '$data_type.fastq_input2.name'
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94 #end if
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96
0
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97 ]]></command>
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98 <inputs>
1
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99 <conditional name="data_type">
0
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100 <param name="type" type="select" label="Specify the read type.">
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101 <option value="single">Single-end Data</option>
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102 <option value="paired">Paired-end Data</option>
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103 <option value="collection">Collection Paired-end Data</option>
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104 </param>
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105 <when value="single">
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106 <param name="fastq_input1" type="data" format="fastqsanger, fastq, fasta" label="Single end read file(s)"/>
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107 </when>
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108 <when value="paired">
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109 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
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110 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
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111 </when>
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112 <when value="collection">
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113 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
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114 </when>
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115 </conditional>
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116 <conditional name="type_of_scheme">
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117 <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)">
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118 <option value="heidelberg">Heidelberg scheme</option>
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119 <option value="enteritidis">Enteritidis scheme</option>
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120 <option value="custom">Specify your own custom scheme</option>
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121 </param>
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122 <when value="heidelberg"/>
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123 <when value="enteritidis"/>
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124 <when value="custom">
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125 <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/>
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126 </when>
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127 </conditional>
3
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128 <!-- K-mer frequencies. -->
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129 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
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130 <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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131 <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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132 </section>
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133 <!-- Quality Checking Parameters -->
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134 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
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135 <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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136 <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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137 <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}"/>
29faaa849e41 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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138 <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}"/>
29faaa849e41 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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139 </section>
0
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140 </inputs>
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141 <outputs>
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142 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
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143 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
3
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144 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
0
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145 </outputs>
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146 <tests>
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147 <test>
1
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148 <param name="type" value="single"/>
0
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149 <param name="type_of_scheme" value="heidelberg"/>
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150 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
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151 <output name="results.tab">
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152 <assert_contents>
3
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153 <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
9407a9eaad22 planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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154 </assert_contents>
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155 </output>
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156 <output name="match_results.tab">
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157 <assert_contents>
3
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158 <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"/>
29faaa849e41 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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159 </assert_contents>
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160 </output>
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161 <output name="tech_results.tab">
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162 <assert_contents>
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163 <has_text_matching expression="sample\s+subtype\s+qc_status\s+qc_message"/>
0
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164 </assert_contents>
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165 </output>
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166 </test>
1
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167 <test>
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168 <param name="type" value="paired"/>
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169 <param name="type_of_scheme" value="heidelberg"/>
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170 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>
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171 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
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172 <output name="results.tab">
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173 <assert_contents>
3
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174 <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"/>
29faaa849e41 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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175 </assert_contents>
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176 </output>
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177 <output name="match_results.tab">
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178 <assert_contents>
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179 <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"/>
29faaa849e41 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c
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180 </assert_contents>
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181 </output>
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182 <output name="tech_results.tab">
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183 <assert_contents>
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184 <has_text_matching expression="sample\s+subtype\s+qc_status\s+qc_message"/>
1
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185 </assert_contents>
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186 </output>
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187 </test>
0
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188 </tests>
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189 <help><![CDATA[
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190 ***********************************************************
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191 bio_hansel - Heidelberg And eNteritidis Snp ELucidation
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192 ***********************************************************
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193
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194 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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195 Subtype *Salmonella* genome assemblies (FASTA files) and/or whole-genome sequencing reads (FASTQ files)!
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196
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197 Usage
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198 =====
1
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199 1) Enter your FASTA/FASTQ file(s)
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200 2) Select which scheme you would like to use (e.g. heidelberg, enteritidis, or specify your own)
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201 3) Click Execute
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202
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203 For more information visit `https://github.com/phac-nml/bio_hansel`
0
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204
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205
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206 Example Usage
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207 =============
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208
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209 Analysis of a single FASTA file
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210 -------------------------------
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211
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212
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213 Contents of ``results.tab``:
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214
1
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215 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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216 | 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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217 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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218 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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219 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
0
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220
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221
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222
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223 Contents of ``match_results.tab``:
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224
1
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225 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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226 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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227 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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228 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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229 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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230 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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231 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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232 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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233 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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234 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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235 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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236 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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237 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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238 | 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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239 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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240 | 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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241 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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242 | 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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243 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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244 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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245 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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246 | 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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247 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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248 | 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 |
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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249 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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250 | 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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251 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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252 | 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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253 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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254
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255 Next 196 lines omitted.
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256
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258
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259 Analysis of a single FASTQ readset
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260 ----------------------------------
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261
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262 Contents of ``results.tab``:
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263
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264 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
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265 | 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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266 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
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267 | 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 |
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268 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
0
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269
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271 Contents of ``match_results.tab``:
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272
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273 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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274 | seq | freq | sample | file_path | tilename | is_pos_tile | subtype | refposition | is_kmer_freq_okay | scheme |
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275 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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276 | ACGGTAAAAGAGGACTTGACTGGCGCGATTTGC | 68 | 564 | forward.fastqsanger; reverse.fastqsanger | 21097-2.2.1.1.1 | True | 2.2.1.1.1 | 21097 | True | heidelberg |
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277 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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278 | AACCGGCGGTATTGGCTGCGGTAAAAGTACCGT | 77 | 564 | forward.fastqsanger; reverse.fastqsanger | 157792-2.2.1.1.1 | True | 2.2.1.1.1 | 157792 | True | heidelberg |
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279 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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280 | CCGCTGCTTTCTGAAATCGCGCGTCGTTTCAAC | 67 | 564 | forward.fastqsanger; reverse.fastqsanger | 293728-2.2.1.1 | True | 2.2.1.1 | 293728 | True | heidelberg |
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281 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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282 | GAATAACAGCAAAGTGATCATGATGCCGCTGGA | 91 | 564 | forward.fastqsanger; reverse.fastqsanger | 607438-2.2.1 | True | 2.2.1 | 607438 | True | heidelberg |
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283 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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284 | CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA | 87 | 564 | forward.fastqsanger; reverse.fastqsanger | 691203-2.2.1.1 | True | 2.2.1.1 | 691203 | True | heidelberg |
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285 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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286 | CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC | 33 | 564 | forward.fastqsanger; reverse.fastqsanger | 944885-2.2.1.1.1 | True | 2.2.1.1.1 | 944885 | True | heidelberg |
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287 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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288
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289 Next 200 lines omitted.
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290
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291 Galaxy wrapper written by Matthew Gopez at the Public Health Agency of Canada, National Microbiology Laboratory.
0
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292
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293 ]]></help>
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294 <citations>
1
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295 <citation type="bibtex">@ARTICLE{a1,
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296 title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},
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297 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Chad R. Laing, 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.},
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298 url = {https://github.com/phac-nml/bio_hansel}
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299 }
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300 }</citation>
0
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301 </citations>
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302 </tool>