annotate staramr_search.xml @ 6:3c09557ac425 draft

planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
author nml
date Tue, 30 Apr 2019 15:50:46 -0400
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children f1adc47e017a
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1 <tool id="staramr_search" name="staramr" version="@VERSION@">
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2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
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3 <macros>
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4 <token name="@VERSION@">0.5.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">staramr</requirement>
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8 </requirements>
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9 <version_command>staramr --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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12
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13 #set $named_genomes = ''
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14 #for $genome in $genomes
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15 #set $_named_genome = re.sub(r'(\s|\(|\))', '_', '"{}.fasta"'.format($genome.element_identifier))
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16 ln -s "$genome" $_named_genome &&
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17 #set $named_genomes = $named_genomes + ' ' + $_named_genome
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18 #end for
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20 #set $excel_proper_extension = '"{}.xlsx"'.format($excel)
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21 ln -s "$excel" $excel_proper_extension &&
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23 staramr search
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25 --nprocs "\${GALAXY_SLOTS:-1}"
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27 --pid-threshold $advanced.pid_threshold
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28 --percent-length-overlap-resfinder $advanced.plength_resfinder
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29 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder
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30 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
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32 $advanced.report_all_blast
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33 $advanced.exclude_negatives
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34 $advanced.exclude_resistance_phenotypes
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35
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36 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
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37 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
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38 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
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39 --no-exclude-genes
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40 #end if
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41
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42 #if str($advanced.plasmidfinder_type) != 'include_all'
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43 --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
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44 #end if
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45
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46 --output-summary $summary
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47 --output-detailed-summary $detailed_summary
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48 --output-resfinder $resfinder
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49 --output-plasmidfinder $plasmidfinder
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50 #if str($use_pointfinder) != 'disabled'
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51 --output-pointfinder $pointfinder
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52 #end if
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53 --output-settings $settings
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54 --output-excel $excel_proper_extension
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56 --output-hits-dir staramr_hits
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57
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58 #if str($use_pointfinder) != 'disabled'
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59 --pointfinder-organism '${use_pointfinder}'
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60 #end if
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62 $named_genomes
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63 ]]></command>
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64 <inputs>
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65 <param type="data" name="genomes" format="fasta" multiple="true"/>
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66 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
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67 <option value="disabled" selected="true">Disable PointFinder</option>
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68 <option value="salmonella">Salmonella</option>
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69 <option value="campylobacter">Campylobacter</option>
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70 </param>
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71 <section name="advanced" title="Advanced options" expanded="false">
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72 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
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73 min="0" max="100" help="(--pid-threshold)" />
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74 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
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75 min="0" max="100" help="(--percent-length-overlap-resfinder)" />
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76 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
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77 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
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78 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0"
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79 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" />
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80 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
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81 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
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82 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
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83 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
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84 <conditional name="exclude_genes">
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85 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
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86 <option value="default" selected="true">Exclude default list of AMR genes</option>
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87 <option value="custom">Provide a custom list of AMR genes to exclude</option>
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88 <option value="none">Do not exclude any AMR genes</option>
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89 </param>
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90 <when value="default" />
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91 <when value="custom">
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92 <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
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93 </when>
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94 <when value="none" />
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95 </conditional>
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96 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
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97 <option value="include_all" selected="true">Include all available database types</option>
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98 <option value="gram_positive">Gram Positive</option>
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99 <option value="enterobacteriaceae">Enterobacteriaceae</option>
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100 </param>
0
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101 </section>
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102 </inputs>
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103 <outputs>
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104 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
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105 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
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106 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
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107 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
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108 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
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109 <filter>use_pointfinder != "disabled"</filter>
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110 </data>
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111 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
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112 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
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113 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
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114 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
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115 </collection>
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116 </outputs>
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117 <tests>
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118 <test>
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119 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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120 <param name="use_pointfinder" value="salmonella" />
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121
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122 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
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123 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
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124 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
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125 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
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126 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
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127 <output_collection name="blast_hits" type="list">
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128 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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129 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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130 </output_collection>
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131 </test>
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132 <test>
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133 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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134
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135 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
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136 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
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137 <output_collection name="blast_hits" type="list">
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138 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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139 </output_collection>
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140 </test>
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141 <test>
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142 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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143 <param name="pid_threshold" value="99.8" />
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144
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145 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
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146 </test>
1
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147 <test>
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148 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
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149 <param name="pid_threshold" value="99.8" />
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150
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151 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
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152 </test>
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153 <test>
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154 <param name="genomes" value="test-aminoglycoside.fsa" />
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155
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156 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
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157 </test>
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158 <test>
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159 <param name="genomes" value="test-aminoglycoside.fsa" />
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160 <param name="exclude_genes_condition" value="none" />
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161
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162 <output name="summary" file="test6-summary.tsv" ftype="tabular" />
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163 </test>
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164 <test>
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165 <param name="genomes" value="test-aminoglycoside.fsa" />
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166 <param name="exclude_genes_condition" value="custom" />
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167 <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
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168
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169 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
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170 </test>
0
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171 </tests>
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172 <help><![CDATA[
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173 staramr
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174 =======
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175
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176 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.
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177
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178 Usage
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179 -----
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180
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181 1. Select your genome contigs (in FASTA format).
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182 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* and *campylobacter* is supported).
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183 3. Run the tool.
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184
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185 Input
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186 -----
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187
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188 Genomes
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189 ```````
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190
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191 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.
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192
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193 Exclude genes file
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194 ``````````````````
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195
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196 Setting **Provide a custom list of AMR genes to exclude** in the **Advanced options** allows you to pass a file containing a list of genes to exclude from the results. The file must start with a line **#gene_id** and the gene names must correspond to the sequence IDs in the ResFinder/PointFinder databases. For example:
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197
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198 ::
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199
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200 #gene_id
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201 aac(6')-Iaa_1_NC_003197
6
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202 ColpVC_1__JX133088
4
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203
0
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204 Output
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205 ------
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206
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207 There are 5 different output files produced by `staramr` as well as a collection of additional files.
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208
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209 summary.tsv
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210 ```````````
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211
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212 A summary of all detected AMR genes/mutations in each genome, one genome per line.
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213
6
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214 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
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215 | Isolate ID | Genotype | Predicted Phenotype | Plasmid Genes |
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216 +============+===========================================================+===========================================================================================================+=====================================+
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217 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 |
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218 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
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219 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 |
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220 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
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221
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222 detailed_summary.tsv
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223 ````````````````````
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224
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225 A detailed summary of all detected AMR genes/mutations/plasmids in each genome, one gene per line.
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226
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227 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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228 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type |
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229 +============+=============+===================================+===========+==========+=========================+=============+========+========+===========+============+
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230 | SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid |
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231 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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232 | SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid |
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233 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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234 | SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid |
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235 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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236 | SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid |
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237 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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238 | SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance |
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239 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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240 | SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance |
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241 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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242 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance |
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243 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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244 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance |
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245 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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246 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance |
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247 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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248 | SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance |
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249 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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250 | SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance |
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251 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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252 | SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid |
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253 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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254 | SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid |
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255 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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256 | SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid |
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257 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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258 | SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid |
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259 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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260 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance |
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261 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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262 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance |
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263 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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264 | SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance |
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265 +------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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266
0
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267
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268 resfinder.tsv
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269 `````````````
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270
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271 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
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272
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273 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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274 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
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275 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
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276 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 |
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277 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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278 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 |
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279 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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280 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 |
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281 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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282 | SRR1952908 | aadA1 | streptomycin | 100.00 | 100.00 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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283 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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284 | SRR1952908 | aadA2 | streptomycin | 99.75 | 100.00 | 792/792 | contig00030 | 7760 | 6969 | JQ364967 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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285 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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286 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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287 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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288 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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289 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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290 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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291 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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292
6
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293 plasmidfinder.tsv
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294 `````````````````
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295
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296 A tabular file of each AMR plasmid gene and additional BLAST information from the **PlasmidFinder** database, one plasmid gene per line.
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297
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298 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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299 | Isolate ID | Gene | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
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300 +============+===========+===========+==========+=========================+=============+=======+=======+===========+
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301 | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 |
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302 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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303 | SRR1952908 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 |
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304 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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305 | SRR1952908 | IncFII(S) | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 |
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306 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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307 | SRR1952908 | IncI1 | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 |
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308 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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309 | SRR1952926 | ColpVC | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 |
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310 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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311 | SRR1952926 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 |
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312 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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313 | SRR1952926 | IncFII(S) | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 |
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314 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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315 | SRR1952926 | IncI1 | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 |
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316 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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317
0
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318 pointfinder.tsv
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319 ```````````````
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320
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321 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
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322
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323 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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324 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End |
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325 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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326 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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327 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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328 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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329 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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330
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331 settings.txt
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332 ````````````
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333
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334 The command-line, database versions, and other settings used to run `staramr`.
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335
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336 ::
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337
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338 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
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339 version = 0.5.0
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340 start_time = 2019-04-25 16:01:32
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341 end_time = 2019-04-25 16:01:34
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342 total_minutes = 0.04
0
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343 resfinder_db_dir = staramr/databases/data/dist/resfinder
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344 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
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345 resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
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346 resfinder_db_date = Mon, 16 Jul 2018 16:58
0
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347 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
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348 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
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349 pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7
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350 pointfinder_db_date = Wed, 04 Jul 2018 14:27
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351 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder
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352 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
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353 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8
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354 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51
0
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355 pointfinder_gene_drug_version = 050218
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356 resfinder_gene_drug_version = 050218.1
0
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357
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358 results.xlsx
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359 ````````````
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360
6
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361 An Excel spreadsheet containing the previous 5 files as separate worksheets.
0
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362
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363 BLAST Hits
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364 ``````````
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365
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366 The dataset collection **hits** stores fasta files of the specific blast hits.
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367
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368 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
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369
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370 .. _staramr: https://github.com/phac-nml/staramr
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371 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
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372 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
0
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373 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
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374 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
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375 ]]></help>
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376 <citations>
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377 <citation type="bibtex">
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378 @misc{githubstaramr,
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379 author = {Petkau, Aaron},
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380 year = {2018},
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381 title = {staramr},
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382 publisher = {GitHub},
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383 journal = {GitHub repository},
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384 url = {https://github.com/phac-nml/staramr},
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385 }</citation>
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386 </citations>
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387 </tool>