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annotate staramr_search.xml @ 5:930893c83a1a draft

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planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
author nml
date Tue, 19 Feb 2019 16:47:25 -0500
parents 1e8ec0f861ff
children 3c09557ac425
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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 and PointFinder databases searching for AMR genes.</description>
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3 <macros>
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4 <token name="@VERSION@">0.4.0</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-pointfinder $advanced.plength_pointfinder
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31 $advanced.report_all_blast
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32 $advanced.exclude_negatives
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33 $advanced.exclude_resistance_phenotypes
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34
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35 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
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36 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
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37 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
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38 --no-exclude-genes
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39 #end if
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40
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41 --output-summary $summary
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42 --output-resfinder $resfinder
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43 #if $use_pointfinder.enable
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44 --output-pointfinder $pointfinder
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45 #end if
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46 --output-settings $settings
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47 --output-excel $excel_proper_extension
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49 --output-hits-dir staramr_hits
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51 #if $use_pointfinder.enable
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52 --pointfinder-organism $use_pointfinder.organism
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53 #end if
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55 $named_genomes
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56 ]]></command>
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57 <inputs>
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58 <param type="data" name="genomes" format="fasta" multiple="true"/>
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59 <conditional name="use_pointfinder">
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60 <param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" />
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61 <when value="true">
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62 <param name="organism" type="select" label="Select a pointfinder organism">
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63 <option value="salmonella" selected="true">Salmonella</option>
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64 <option value="campylobacter">Campylobacter</option>
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65 </param>
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66 </when>
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67 <when value="false" />
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68 </conditional>
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69 <section name="advanced" title="Advanced options" expanded="false">
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70 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
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71 min="0" max="100" help="(--pid-threshold)" />
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72 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
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73 min="0" max="100" help="(--percent-length-overlap-resfinder)" />
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74 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
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75 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
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76 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
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77 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
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78 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
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79 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
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80 <conditional name="exclude_genes">
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81 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
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82 <option value="default" selected="true">Exclude default list of AMR genes</option>
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83 <option value="custom">Provide a custom list of AMR genes to exclude</option>
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84 <option value="none">Do not exclude any AMR genes</option>
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85 </param>
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86 <when value="default" />
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87 <when value="custom">
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88 <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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89 </when>
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90 <when value="none" />
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91 </conditional>
0
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92 </section>
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93 </inputs>
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94 <outputs>
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95 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
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96 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
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97 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
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98 <filter>use_pointfinder['enable']</filter>
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99 </data>
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100 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
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101 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
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102 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
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103 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
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104 </collection>
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105 </outputs>
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106 <tests>
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107 <test>
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108 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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109 <conditional name="use_pointfinder">
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110 <param name="enable" value="true" />
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111 <param name="organism" value="salmonella" />
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112 </conditional>
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113
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114 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
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115 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
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116 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
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117 <output_collection name="blast_hits" type="list">
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118 <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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119 <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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120 </output_collection>
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121 </test>
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122 <test>
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123 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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124
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125 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
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126 <output name="resfinder" file="test2-resfinder.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="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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129 </output_collection>
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130 </test>
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131 <test>
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132 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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133 <param name="pid_threshold" value="99.8" />
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134
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135 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
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136 </test>
1
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137 <test>
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138 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
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139 <param name="pid_threshold" value="99.8" />
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140
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141 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
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142 </test>
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143 <test>
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144 <param name="genomes" value="test-aminoglycoside.fsa" />
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145
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146 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
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147 </test>
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148 <test>
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149 <param name="genomes" value="test-aminoglycoside.fsa" />
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150 <param name="exclude_genes_condition" value="none" />
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151
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152 <output name="summary" file="test6-summary.tsv" ftype="tabular" />
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153 </test>
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154 <test>
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155 <param name="genomes" value="test-aminoglycoside.fsa" />
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156 <param name="exclude_genes_condition" value="custom" />
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157 <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
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158
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159 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
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160 </test>
0
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161 </tests>
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162 <help><![CDATA[
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163 staramr
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164 =======
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165
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166 staramr_ scans bacterial genome contigs against both the ResFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.
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167
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168 Usage
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169 -----
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170
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171 1. Select your genome contigs (in FASTA format).
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172 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).
0
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173 3. Run the tool.
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174
4
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175 Input
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176 -----
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177
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178 Genomes
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179 ```````
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180
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181 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.
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182
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183 Exclude genes file
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184 ``````````````````
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185
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186 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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187
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188 ::
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189
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190 #gene_id
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191 aac(6')-Iaa_1_NC_003197
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192
0
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193 Output
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194 ------
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195
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196 There are 5 different output files produced by `staramr` as well as a collection of additional files.
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197
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198 summary.tsv
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199 ```````````
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200
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201 A summary of all detected AMR genes/mutations in each genome, one genome per line.
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202
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203 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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204 | Isolate ID | Genotype | Predicted Phenotype |
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205 +============+===========================================================+===========================================================================================================+
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206 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline |
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207 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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208 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline |
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209 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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210
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211 resfinder.tsv
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212 `````````````
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213
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214 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
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215
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216 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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217 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
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218 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
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219 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 |
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220 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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221 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 |
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222 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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223 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 |
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224 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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225 | SRR1952908 | aadA1 | streptomycin | 100.00 | 100.00 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 |
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226 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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227 | SRR1952908 | aadA2 | streptomycin | 99.75 | 100.00 | 792/792 | contig00030 | 7760 | 6969 | JQ364967 |
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228 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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229 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 |
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230 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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231 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 |
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232 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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233 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 |
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234 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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235
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236 pointfinder.tsv
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237 ```````````````
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238
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239 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
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240
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241 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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242 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End |
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243 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
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244 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 |
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245 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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246 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 |
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247 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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248
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249 settings.txt
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250 ````````````
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251
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252 The command-line, database versions, and other settings used to run `staramr`.
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253
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254 ::
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255
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256 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
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257 version = 0.2.0
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258 start_time = 2018-06-05 14:41:44
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259 end_time = 2018-06-05 14:41:47
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260 total_minutes = 0.05
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261 resfinder_db_dir = staramr/databases/data/dist/resfinder
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262 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
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263 resfinder_db_commit = dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2
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264 resfinder_db_date = Tue, 20 Mar 2018 16:49
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265 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
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266 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
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267 pointfinder_db_commit = ba65c4d175decdc841a0bef9f9be1c1589c0070a
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268 pointfinder_db_date = Fri, 06 Apr 2018 09:02
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269 pointfinder_gene_drug_version = 050218
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270 resfinder_gene_drug_version = 050218
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271
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272 results.xlsx
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273 ````````````
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274
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275 An Excel spreadsheet containing the previous 4 files as separate worksheets.
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276
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277 BLAST Hits
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278 ``````````
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279
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280 The dataset collection **hits** stores fasta files of the specific blast hits.
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281
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282 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
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283
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284 .. _staramr: https://github.com/phac-nml/staramr
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285 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
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286 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
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287 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
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288 ]]></help>
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289 <citations>
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290 <citation type="bibtex">
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291 @misc{githubstaramr,
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292 author = {Petkau, Aaron},
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293 year = {2018},
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294 title = {staramr},
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295 publisher = {GitHub},
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296 journal = {GitHub repository},
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297 url = {https://github.com/phac-nml/staramr},
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298 }</citation>
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299 </citations>
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300 </tool>