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annotate bio_hansel.xml @ 5:6396d043667b draft

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planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
author nml
date Wed, 21 Feb 2018 12:13:32 -0500
parents c0d08ba0c6ee
children 5a42e475436e
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6396d043667b planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
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1 <tool id="bio_hansel" name="Bio Hansel" version="1.2.0">
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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="1.2.0">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' '$data_type.fastq_input1.name'.fastq &&
6396d043667b planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
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12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name'.fastq &&
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14 #elif $data_type.type == "collection":
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5
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16 ln -s '$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 $data_type.fastq_input1.is_of_type('fastq'):
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6396d043667b planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
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22 ln -s '$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.
9407a9eaad22 planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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33 #if $type_of_scheme.scheme_type == "custom":
9407a9eaad22 planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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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
9407a9eaad22 planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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40 hansel
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43 ## Select the scheme
9407a9eaad22 planemo upload for repository https://github.com/phac-nml/bio_hansel commit c35a4502f95471e22dea2d77f36b92c47424cecc
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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 ## Adding more parameters to the command.
3
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84 -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab
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86
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87 ## Entering the file inputs
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88
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89 #if $data_type.type == "single":
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91 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
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92 '$data_type.fastq_input1.name'.fastq
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93 #end if
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94
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95 #if $data_type.fastq_input1.is_of_type('fasta'):
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96 '$data_type.fastq_input1.name'.fasta
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97 #end if
0
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98
1
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99 #elif $data_type.type =="collection":
5
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100 -p '$data_type.fastq_input1.name'_1.fastq '$data_type.fastq_input1.name'_2.fastq
1
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101
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102 #elif $data_type.type =="paired":
5
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103 -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq
0
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104
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105 #end if
1
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106
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107
0
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108 ]]></command>
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109 <inputs>
1
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110 <conditional name="data_type">
0
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111 <param name="type" type="select" label="Specify the read type.">
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112 <option value="single">Single-end Data</option>
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113 <option value="paired">Paired-end Data</option>
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114 <option value="collection">Collection Paired-end Data</option>
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115 </param>
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116 <when value="single">
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117 <param name="fastq_input1" type="data" format="fastqsanger, fastq, fasta" label="Single end read file(s)"/>
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118 </when>
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119 <when value="paired">
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120 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
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121 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
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122 </when>
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123 <when value="collection">
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124 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
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125 </when>
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126 </conditional>
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127 <conditional name="type_of_scheme">
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128 <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)">
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129 <option value="heidelberg">Heidelberg scheme</option>
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130 <option value="enteritidis">Enteritidis scheme</option>
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131 <option value="custom">Specify your own custom scheme</option>
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132 </param>
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133 <when value="heidelberg"/>
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134 <when value="enteritidis"/>
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135 <when value="custom">
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136 <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/>
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137 </when>
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138 </conditional>
3
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139 <!-- K-mer frequencies. -->
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140 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
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141 <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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142 <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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143 </section>
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144 <!-- Quality Checking Parameters -->
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145 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
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146 <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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147 <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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148 <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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149 <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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150 </section>
5
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151 <section name="dev_args" title="Developer Options" expanded="False">
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152 <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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153 <option value="no">no</option>
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154 <option value="yes">yes</option>
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155 </param>
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156 </section>
0
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157 </inputs>
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158 <outputs>
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159 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
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160 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
3
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161 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
5
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162 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
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163 <filter>dev_args['use_json'] == "yes"</filter>
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164 </data>
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165 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
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166 <filter>dev_args['use_json'] == "yes"</filter>
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167 </data>
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168 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
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169 <filter>dev_args['use_json'] == "yes"</filter>
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170 </data>
0
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171 </outputs>
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172 <tests>
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173 <test>
1
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174 <param name="type" value="single"/>
0
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175 <param name="type_of_scheme" value="heidelberg"/>
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176 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
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177 <output name="results.tab">
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178 <assert_contents>
5
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179 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\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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180 </assert_contents>
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181 </output>
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182 <output name="match_results.tab">
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183 <assert_contents>
3
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184 <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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185 </assert_contents>
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186 </output>
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187 <output name="tech_results.tab">
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188 <assert_contents>
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189 <has_text_matching expression="sample\s+subtype\s+qc_status\s+qc_message"/>
0
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190 </assert_contents>
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191 </output>
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192 </test>
1
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193 <test>
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194 <param name="type" value="paired"/>
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195 <param name="type_of_scheme" value="heidelberg"/>
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196 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>
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197 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
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198 <output name="results.tab">
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199 <assert_contents>
5
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200 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\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"/>
3
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201 </assert_contents>
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202 </output>
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203 <output name="match_results.tab">
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204 <assert_contents>
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205 <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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206 </assert_contents>
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207 </output>
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208 <output name="tech_results.tab">
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209 <assert_contents>
5
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210 <has_text_matching expression="sample\s+subtype\s+avg_tile_coverage\s+qc_status\s+qc_message"/>
1
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211 </assert_contents>
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212 </output>
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213 </test>
0
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214 </tests>
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215 <help><![CDATA[
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216 ***********************************************************
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217 bio_hansel - Heidelberg And eNteritidis Snp ELucidation
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218 ***********************************************************
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219
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220 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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221 Subtype *Salmonella* genome assemblies (FASTA files) and/or whole-genome sequencing reads (FASTQ files)!
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222
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223 Usage
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224 =====
1
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225 1) Enter your FASTA/FASTQ file(s)
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226 2) Select which scheme you would like to use (e.g. heidelberg, enteritidis, or specify your own)
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227 3) Click Execute
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228
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229 For more information visit `https://github.com/phac-nml/bio_hansel`
0
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230
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231
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232 Example Usage
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233 =============
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234
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235 Analysis of a single FASTA file
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236 -------------------------------
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237
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238
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239 Contents of ``results.tab``:
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240
1
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241 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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242 | 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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243 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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244 | 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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245 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
0
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246
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247
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248
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249 Contents of ``match_results.tab``:
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250
1
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251 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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252 | 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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253 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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254 | 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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255 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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256 | 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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257 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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258 | 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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259 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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260 | 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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261 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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262 | 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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263 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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264 | 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 |
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265 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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266 | 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 |
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267 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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268 | 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 |
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269 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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270 | 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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271 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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272 | 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 |
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273 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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274 | 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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275 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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276 | 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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277 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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278 | 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 |
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279 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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280
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281 Next 196 lines omitted.
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282
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283
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284
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285 Analysis of a single FASTQ readset
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286 ----------------------------------
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287
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288 Contents of ``results.tab``:
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289
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290 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
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291 | 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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292 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
ba271365095e planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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293 | 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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294 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
0
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295
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297 Contents of ``match_results.tab``:
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298
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299 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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300 | seq | freq | sample | file_path | tilename | is_pos_tile | subtype | refposition | is_kmer_freq_okay | scheme |
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301 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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302 | 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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303 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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304 | 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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305 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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306 | 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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307 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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308 | GAATAACAGCAAAGTGATCATGATGCCGCTGGA | 91 | 564 | forward.fastqsanger; reverse.fastqsanger | 607438-2.2.1 | True | 2.2.1 | 607438 | True | heidelberg |
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309 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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310 | 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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311 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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312 | 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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313 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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314
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315 Next 200 lines omitted.
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316
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317 Galaxy wrapper written by Matthew Gopez at the Public Health Agency of Canada, National Microbiology Laboratory.
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318
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319 ]]></help>
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320 <citations>
1
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321 <citation type="bibtex">@ARTICLE{a1,
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322 title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},
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323 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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324 url = {https://github.com/phac-nml/bio_hansel}
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325 }
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326 }</citation>
0
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327 </citations>
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328 </tool>