annotate staramr_search.xml @ 0:fef5aff062c7 draft

planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
author nml
date Wed, 06 Jun 2018 14:20:58 -0400
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children 3801ea82c888
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fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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1 <tool id="staramr_search" name="staramr" version="0.2.0">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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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 <requirements>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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4 <requirement type="package" version="0.2.0">staramr</requirement>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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5 </requirements>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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6 <command detect_errors="exit_code"><![CDATA[
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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7 #set $named_genomes = ''
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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8 #for $genome in $genomes
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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9 #set $_named_genome = '"{}.fasta"'.format($genome.element_identifier)
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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10 ln -s "$genome" $_named_genome &&
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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11 #set $named_genomes = $named_genomes + ' ' + $_named_genome
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12 #end for
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13
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14 #set $excel_proper_extension = '"{}.xlsx"'.format($excel)
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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15 ln -s "$excel" $excel_proper_extension &&
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17 staramr search
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19 --nprocs "\${GALAXY_SLOTS:-1}"
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21 --pid-threshold $advanced.pid_threshold
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22 --percent-length-overlap-resfinder $advanced.plength_resfinder
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23 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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25 $advanced.report_all_blast
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26 $advanced.exclude_negatives
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27 $advanced.exclude_resistance_phenotypes
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28
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29 --output-summary $summary
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30 --output-resfinder $resfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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31 #if $use_pointfinder.enable
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32 --output-pointfinder $pointfinder
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33 #end if
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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34 --output-settings $settings
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35 --output-excel $excel_proper_extension
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36
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37 --output-hits-dir staramr_hits
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38
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39 #if $use_pointfinder.enable
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40 --pointfinder-organism $use_pointfinder.organism
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41 #end if
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42
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43 $named_genomes
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44 ]]></command>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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45 <inputs>
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46 <param type="data" name="genomes" format="fasta" multiple="true"/>
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47 <conditional name="use_pointfinder">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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48 <param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" />
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49 <when value="true">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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50 <param name="organism" type="select" label="Select a pointfinder organism">
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51 <option value="salmonella" selected="true">Salmonella</option>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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52 </param>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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53 </when>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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54 <when value="false" />
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55 </conditional>
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56 <section name="advanced" title="Advanced options" expanded="false">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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57 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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58 min="0" max="100" help="(--pid-threshold)" />
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59 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
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60 min="0" max="100" help="(--percent-length-overlap-resfinder)" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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61 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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62 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
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63 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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64 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
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65 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
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66 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
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67 </section>
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68 </inputs>
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69 <outputs>
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70 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
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71 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
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72 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
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73 <filter>use_pointfinder['enable']</filter>
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74 </data>
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75 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
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76 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
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77 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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78 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
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79 </collection>
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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84 <conditional name="use_pointfinder">
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85 <param name="enable" value="true" />
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86 <param name="organism" value="salmonella" />
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87 </conditional>
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88
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89 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
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90 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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91 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
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92 <output_collection name="blast_hits" type="list">
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93 <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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94 <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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95 </output_collection>
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96 </test>
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97 <test>
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98 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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99
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100 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
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101 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
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102 <output_collection name="blast_hits" type="list">
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103 <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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104 </output_collection>
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105 </test>
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106 <test>
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107 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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108 <param name="pid_threshold" value="99.8" />
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109
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110 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
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111 </test>
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112 </tests>
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113 <help><![CDATA[
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114 staramr
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115 =======
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116
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117 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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118
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119 Usage
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120 -----
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121
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122 1. Select your genome contigs (in FASTA format).
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123 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* is supported).
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124 3. Run the tool.
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125
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126 Output
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127 ------
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128
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129 There are 5 different output files produced by `staramr` as well as a collection of additional files.
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130
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131 summary.tsv
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132 ```````````
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133
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134 A summary of all detected AMR genes/mutations in each genome, one genome per line.
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135
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136 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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137 | Isolate ID | Genotype | Predicted Phenotype |
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138 +============+===========================================================+===========================================================================================================+
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139 | 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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140 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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141 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline |
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142 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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143
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144 resfinder.tsv
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145 `````````````
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146
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147 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
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148
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149 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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150 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
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151 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
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152 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 |
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153 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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154 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 |
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155 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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156 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 |
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157 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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158 | SRR1952908 | aadA1 | streptomycin | 100.00 | 100.00 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 |
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159 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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160 | SRR1952908 | aadA2 | streptomycin | 99.75 | 100.00 | 792/792 | contig00030 | 7760 | 6969 | JQ364967 |
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161 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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162 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 |
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163 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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164 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 |
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165 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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166 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 |
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167 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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168
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169 pointfinder.tsv
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170 ```````````````
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171
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172 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
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173
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174 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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175 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End |
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176 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
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177 | 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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178 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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179 | 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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180 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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181
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182 settings.txt
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183 ````````````
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184
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185 The command-line, database versions, and other settings used to run `staramr`.
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186
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187 ::
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188
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189 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
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190 version = 0.2.0
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191 start_time = 2018-06-05 14:41:44
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192 end_time = 2018-06-05 14:41:47
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193 total_minutes = 0.05
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194 resfinder_db_dir = staramr/databases/data/dist/resfinder
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195 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
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196 resfinder_db_commit = dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2
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197 resfinder_db_date = Tue, 20 Mar 2018 16:49
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198 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
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199 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
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200 pointfinder_db_commit = ba65c4d175decdc841a0bef9f9be1c1589c0070a
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201 pointfinder_db_date = Fri, 06 Apr 2018 09:02
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202 pointfinder_gene_drug_version = 050218
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203 resfinder_gene_drug_version = 050218
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204
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205 results.xlsx
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206 ````````````
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207
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208 An Excel spreadsheet containing the previous 4 files as separate worksheets.
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209
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210 BLAST Hits
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211 ``````````
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212
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213 The dataset collection **hits** stores fasta files of the specific blast hits.
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214
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215 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
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216
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217 .. _staramr: https://github.com/phac-nml/staramr
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218 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
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219 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
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220 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
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221 ]]></help>
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222 <citations>
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223 <citation type="bibtex">
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224 @misc{githubstaramr,
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225 author = {Petkau, Aaron},
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226 year = {2018},
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227 title = {staramr},
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228 publisher = {GitHub},
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229 journal = {GitHub repository},
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230 url = {https://github.com/phac-nml/staramr},
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231 }</citation>
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232 </citations>
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233 </tool>