Mercurial > repos > nml > mob_suite

annotate mob_recon.xml @ 8:53f50adcb78e draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit 314c26f1f5e22511c6f406cd9b7108f873cec295"
author nml
date Sat, 28 Nov 2020 20:38:47 +0000
parents 822575bf359f
children
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1 <tool id="mob_recon" name="MOB-Recon" version="@VERSION@+galaxy0">
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2 <description>Type contigs and extract plasmid sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <version_command>mob_recon --version</version_command>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 #import re
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11 #import os.path
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13 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta')
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14 ln -s '$input' '$named_input' &&
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17 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile '${named_input}' --run_typer
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19 #if $adv_param.unicycler_contigs:
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20 --unicycler_contigs
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21 #end if
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23 #if $adv_param.run_overhang:
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24 --run_overhang
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25 #end if
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27 #if $adv_param.debug:
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28 --debug
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29 #end if
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31 #if $adv_param.plasmid_db
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32 --plasmid_db '$adv_param.plasmid_db'
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33 #end if
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35 #if $adv_param.plasmid_mash_db
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36 --plasmid_mash_db '$adv_param.plasmid_mash_db'
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37 #end if
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39 #if $adv_param.plasmid_meta
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40 --plasmid_meta '$adv_param.plasmid_meta'
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41 #end if
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43 #if $adv_param.repetitive_mask
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44 --repetitive_mask '$adv_param.repetitive_mask'
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45 #end if
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47 #if $adv_param.plasmid_mob
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48 --plasmid_mob '$adv_param.plasmid_mob'
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49 #end if
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51 #if $adv_param.plasmid_mpf
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52 --plasmid_mpf '$adv_param.plasmid_mpf'
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53 #end if
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55 #if $adv_param.plasmid_orit
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56 --plasmid_orit '$adv_param.plasmid_orit'
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57 #end if
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59 --min_length '${adv_param.min_length}'
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60 --min_rep_evalue '${adv_param.min_rep_evalue}'
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61 --min_rep_evalue '${adv_param.min_rep_evalue}'
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62 --min_mob_evalue '${adv_param.min_mob_evalue}'
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63 --min_con_evalue '${adv_param.min_con_evalue}'
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64 --min_rep_ident '${adv_param.min_rep_ident}'
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65 --min_mob_ident '${adv_param.min_mob_ident}'
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66 --min_con_ident '${adv_param.min_con_ident}'
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67 --min_rpp_ident '${adv_param.min_rpp_ident}'
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69 --min_rep_cov '${adv_param.min_rep_cov}'
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70 --min_mob_cov '${adv_param.min_mob_cov}'
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71 --min_con_cov '${adv_param.min_con_cov}'
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72 --min_rpp_cov '${adv_param.min_rpp_cov}'
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73 --outdir 'outdir' &&
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74 mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)
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75 ]]>
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76 </command>
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77 <inputs>
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78 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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79 <section name="adv_param" title="Advanced parameters" expanded="False">
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80 <param name="unicycler_contigs" type="boolean" truevalue="true" falsevalue="" checked="true" label="Check for circularity flag generated by unicycler in contigs fasta headers?"/>
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81 <param name="run_overhang" type="boolean" truevalue="true" falsevalue="" checked="true" label="Detect circular contigs (i.e. potential plasmids) with assembly overhangs?"/>
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82 <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?"/>
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83
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84 <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/>
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85 <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001"/>
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86 <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001"/>
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87 <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001"/>
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88 <param name="min_length" label="Minimum length of contigs to classify" type="integer" value="1000"/>
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89 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
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90 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
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91 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/>
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92 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/>
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93
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94 <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80"/>
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95 <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80"/>
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96 <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer" min="0" max="100" value="60"/>
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97 <param name="min_rpp_cov" label="Minimum percentage coverage of contigs by repetitive elements" type="integer" min="0" max="100" value="80"/>
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98
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99 <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/>
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100 <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="MASH sketch of the reference plasmids database"/>
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101 <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help=""/>
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102 <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help=""/>
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103 <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help=""/>
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104 <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help=""/>
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105 <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help=""/>
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106 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help=""/>
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107 </section>
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108 </inputs>
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109 <outputs>
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110 <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/>
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111 <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_results.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>
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112 <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/>
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113 <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids">
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114 <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />
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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="input" value="Ecoli_strain_KV7_complete_LT795502.fasta" ftype="fasta"/>
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120 <section name="adv_param">
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121 <param name="unicycler_contigs" value="True"/>
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122 <param name="run_overhang" value="True"/>
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123 </section>
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124 <output name="contig_report">
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125 <assert_contents>
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126 <has_text text="chromosome"/>
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127 <has_text text="plasmid"/>
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128 <has_text text="IncHI1A"/>
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129 <has_text text="IncN"/>
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130 </assert_contents>
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131 </output>
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132 <output name="mobtyper_aggregate_report">
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133 <assert_contents>
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134 <has_text text="conjugative"/>
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135 <has_text text="Gammaproteobacteria"/>
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136 <has_text text="223020"/>
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137 </assert_contents>
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138 </output>
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139 </test>
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140 </tests>
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141 <help>
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142
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143 **Syntax**
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144
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145 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
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146
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147 For more information please visit https://github.com/phac-nml/mob-suite/.
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148
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149 **Workflow**
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150
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151 This preliminary \"Mobilome and Resistome Analysis Workflow\" linking mob_recon with staramr provides reports on mobilome and resistome for a given isolate given a draft genome assembly. The workflow is located in Shared Data --> Workflows --> Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR). The workflow file can also be manually downloaded from https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/workflows/AMRworkflow_STARAMR.ga.
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152
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153 -----
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154
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155 **Input:**
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156
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157 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
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158
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159
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160 **Output:**
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161
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162 Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
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163
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164 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
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165
0
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166
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167 </help>
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168 <citations>
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169 <citation type="bibtex">
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170 @misc{githubmob-suite,
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171 author = {Robertson J, Nash J},
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172 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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173 publisher = {GitHub},
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174 journal = {GitHub repository},
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175 doi = {10.1099/mgen.0.000206},
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176 url = {https://github.com/phac-nml/mob-suite}
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177 }</citation>
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178 </citations>
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179 </tool>