annotate staramr_search.xml @ 15:be818ae858e4 draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
author nml
date Wed, 22 Jun 2022 14:44:55 +0000
parents 4b9a8031ab74
children 4d83eccf5f81
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1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">
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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@">0.8.0</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 <!-- The staramr conda package includes the mlst software, but the list of schemes
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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9 changes depending on the version. I specify the exact version here to make sure
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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10 the list of schemes provided is consistent -->
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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11 <requirement type="package" version="2.22.0">mlst</requirement>
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12 </requirements>
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13 <version_command>staramr --version</version_command>
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14 <command detect_errors="exit_code"><![CDATA[
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15 #import re
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17 #set $named_genomes = ''
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18 #for $genome in $genomes
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19 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier))
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20 ln -s '$genome' $_named_genome &&
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21 #set $named_genomes = $named_genomes + ' ' + $_named_genome
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22 #end for
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23
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24 #set $excel_proper_extension = 'results.xlsx'
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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25 ln -s '$excel' $excel_proper_extension &&
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27 staramr search
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29 --nprocs "\${GALAXY_SLOTS:-1}"
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30
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7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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31 --genome-size-lower-bound $advanced.genome_size_lower_bound
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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32 --genome-size-upper-bound $advanced.genome_size_upper_bound
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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33 --minimum-N50-value $advanced.minimum_N50_value
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34 --minimum-contig-length $advanced.minimum_contig_length
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35 --unacceptable-number-contigs $advanced.unacceptable_number_contigs
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36
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37 --pid-threshold $advanced.pid_threshold
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38 --percent-length-overlap-resfinder $advanced.plength_resfinder
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39 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder
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40 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
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41
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2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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42 #if str($advanced.mlst_scheme) != 'auto':
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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43 --mlst-scheme '${advanced.mlst_scheme}'
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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44 #end if
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45
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46 $advanced.report_all_blast
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47 $advanced.exclude_negatives
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48 $advanced.exclude_resistance_phenotypes
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49
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50 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
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51 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
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52 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
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53 --no-exclude-genes
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54 #end if
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55
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56 #if str($advanced.plasmidfinder_type) != 'include_all'
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57 --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
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58 #end if
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59
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60 --output-summary '$summary'
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61 --output-detailed-summary '$detailed_summary'
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62 --output-resfinder '$resfinder'
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63 --output-plasmidfinder '$plasmidfinder'
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64 --output-settings '$settings'
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65 --output-excel '$excel_proper_extension'
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66 --output-mlst '$mlst'
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67
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68 --output-hits-dir staramr_hits
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69
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70 #if str($pointfinder_db.use_pointfinder) != 'disabled'
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71 --output-pointfinder '$pointfinder'
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72 #if str($pointfinder_db.use_pointfinder) == 'custom'
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73 --pointfinder-organism '${pointfinder_db.pointfinder_custom}'
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74 #else
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75 --pointfinder-organism '${pointfinder_db.use_pointfinder}'
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76 #end if
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77 #end if
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78
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79 $named_genomes
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80 ]]></command>
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81 <inputs>
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82 <param type="data" name="genomes" format="fasta" multiple="true"/>
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83 <conditional name="pointfinder_db">
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84 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
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85 <option value="disabled" selected="true">Disable PointFinder</option>
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86 <option value="salmonella">Salmonella</option>
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87 <option value="campylobacter">Campylobacter</option>
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88 <option value="custom">Unvalidated</option>
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89 </param>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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90 <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism -->
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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91 <when value="disabled"/>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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parents: 14
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92 <when value="salmonella"/>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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parents: 14
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93 <when value="campylobacter"/>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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parents: 14
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94
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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95 <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms -->
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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96 <when value="custom">
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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97 <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results.">
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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98 <option value="enterococcus_faecalis">enterococcus_faecalis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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99 <option value="enterococcus_faecium">enterococcus_faecium</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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100 <option value="escherichia_coli" selected="true">escherichia_coli</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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101 <option value="helicobacter_pylori">helicobacter_pylori</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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102 <option value="klebsiella">klebsiella</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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103 <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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104 <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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105 <option value="plasmodium_falciparum">plasmodium_falciparum</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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106 <option value="staphylococcus_aureus">staphylococcus_aureus</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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107 </param>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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108 </when>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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109 </conditional>
0
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110 <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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111 <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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112 min="0" max="100" help="(--pid-threshold)" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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113 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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114 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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115 <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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116 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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117 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0"
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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118 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" />
10
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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119 <param name="genome_size_lower_bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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120 help="(--genome-size-lower-bound)" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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121 <param name="genome_size_upper_bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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122 help="(--genome-size-upper-bound)" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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123 <param name="minimum_N50_value" type="integer" label="The minimum N50 value for the quality metrics" value="10000"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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124 help="(--minimum-N50-value)" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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125 <param name="minimum_contig_length" type="integer" label="The minimum contig length for the quality metrics" value="300"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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126 help="(--minimum-contig-length)" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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127 <param name="unacceptable_number_contigs" type="integer" label="The number of contigs, under the minimum contig length which is unacceptable for the quality metrics" value="1000"
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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128 help="(--unacceptable-number-contigs)" />
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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129 <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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130 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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131 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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132 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
13
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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133 <param name="mlst_scheme" type="select" label="MLST Scheme">
15
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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134 <option value="auto" selected="true">Automatic</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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135 <option value="aactinomycetemcomitans">aactinomycetemcomitans</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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136 <option value="abaumannii">abaumannii</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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137 <option value="abaumannii_2">abaumannii_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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138 <option value="achromobacter">achromobacter</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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139 <option value="aeromonas">aeromonas</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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140 <option value="aphagocytophilum">aphagocytophilum</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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141 <option value="arcobacter">arcobacter</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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142 <option value="bbacilliformis">bbacilliformis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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143 <option value="bcc">bcc</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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144 <option value="bcereus">bcereus</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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145 <option value="bfragilis">bfragilis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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146 <option value="bhenselae">bhenselae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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147 <option value="blicheniformis_14">blicheniformis_14</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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148 <option value="bordetella_3">bordetella_3</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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149 <option value="borrelia">borrelia</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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150 <option value="bpseudomallei">bpseudomallei</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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151 <option value="brachyspira">brachyspira</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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152 <option value="brachyspira_2">brachyspira_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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153 <option value="brachyspira_3">brachyspira_3</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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154 <option value="brachyspira_4">brachyspira_4</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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155 <option value="brachyspira_5">brachyspira_5</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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156 <option value="brucella">brucella</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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157 <option value="bsubtilis">bsubtilis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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158 <option value="bwashoensis">bwashoensis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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159 <option value="campylobacter">campylobacter</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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160 <option value="campylobacter_nonjejuni">campylobacter_nonjejuni</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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161 <option value="campylobacter_nonjejuni_2">campylobacter_nonjejuni_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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162 <option value="campylobacter_nonjejuni_3">campylobacter_nonjejuni_3</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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163 <option value="campylobacter_nonjejuni_4">campylobacter_nonjejuni_4</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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164 <option value="campylobacter_nonjejuni_5">campylobacter_nonjejuni_5</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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165 <option value="campylobacter_nonjejuni_6">campylobacter_nonjejuni_6</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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166 <option value="campylobacter_nonjejuni_7">campylobacter_nonjejuni_7</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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167 <option value="campylobacter_nonjejuni_8">campylobacter_nonjejuni_8</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
168 <option value="campylobacter_nonjejuni_9">campylobacter_nonjejuni_9</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
169 <option value="cbotulinum">cbotulinum</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
170 <option value="cdifficile">cdifficile</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
171 <option value="cfreundii">cfreundii</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
172 <option value="chlamydiales">chlamydiales</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
173 <option value="cmaltaromaticum">cmaltaromaticum</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
174 <option value="cperfringens">cperfringens</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
175 <option value="cronobacter">cronobacter</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
176 <option value="csepticum">csepticum</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
177 <option value="diphtheria_3">diphtheria_3</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
178 <option value="dnodosus">dnodosus</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
179 <option value="ecloacae">ecloacae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
180 <option value="ecoli">ecoli</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
181 <option value="ecoli_achtman_4">ecoli_achtman_4</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
182 <option value="edwardsiella">edwardsiella</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
183 <option value="efaecalis">efaecalis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
184 <option value="efaecium">efaecium</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
185 <option value="fpsychrophilum">fpsychrophilum</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
186 <option value="gallibacterium">gallibacterium</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
187 <option value="geotrichum">geotrichum</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
188 <option value="hcinaedi">hcinaedi</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
189 <option value="helicobacter">helicobacter</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
190 <option value="hinfluenzae">hinfluenzae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
191 <option value="hparasuis">hparasuis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
192 <option value="hsuis">hsuis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
193 <option value="kaerogenes">kaerogenes</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
194 <option value="kingella">kingella</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
195 <option value="klebsiella">klebsiella</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
196 <option value="koxytoca">koxytoca</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
197 <option value="leptospira">leptospira</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
198 <option value="leptospira_2">leptospira_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
199 <option value="leptospira_3">leptospira_3</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
200 <option value="liberibacter">liberibacter</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
201 <option value="listeria_2">listeria_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
202 <option value="llactis_phage">llactis_phage</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
203 <option value="lsalivarius">lsalivarius</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
204 <option value="mabscessus">mabscessus</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
205 <option value="magalactiae">magalactiae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
206 <option value="manserisalpingitidis">manserisalpingitidis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
207 <option value="mbovis_2">mbovis_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
208 <option value="mcanis">mcanis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
209 <option value="mcaseolyticus">mcaseolyticus</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
210 <option value="mcatarrhalis_achtman_6">mcatarrhalis_achtman_6</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
211 <option value="mflocculare">mflocculare</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
212 <option value="mgallisepticum">mgallisepticum</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
213 <option value="mgallisepticum_2">mgallisepticum_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
214 <option value="mhaemolytica">mhaemolytica</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
215 <option value="mhominis_3">mhominis_3</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
216 <option value="mhyopneumoniae">mhyopneumoniae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
217 <option value="mhyorhinis">mhyorhinis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
218 <option value="miowae">miowae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
219 <option value="mplutonius">mplutonius</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
220 <option value="mpneumoniae">mpneumoniae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
221 <option value="msciuri">msciuri</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
222 <option value="msynoviae">msynoviae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
223 <option value="mycobacteria_2">mycobacteria_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
224 <option value="neisseria">neisseria</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
225 <option value="oralstrep">oralstrep</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
226 <option value="orhinotracheale">orhinotracheale</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
227 <option value="otsutsugamushi">otsutsugamushi</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
228 <option value="pacnes_3">pacnes_3</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
229 <option value="paeruginosa">paeruginosa</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
230 <option value="pdamselae">pdamselae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
231 <option value="pfluorescens">pfluorescens</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
232 <option value="pgingivalis">pgingivalis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
233 <option value="plarvae">plarvae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
234 <option value="pmultocida">pmultocida</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
235 <option value="pmultocida_2">pmultocida_2</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
236 <option value="ppentosaceus">ppentosaceus</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
237 <option value="pputida">pputida</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
238 <option value="psalmonis">psalmonis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
239 <option value="ranatipestifer">ranatipestifer</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
240 <option value="rhodococcus">rhodococcus</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
241 <option value="sagalactiae">sagalactiae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
242 <option value="saureus">saureus</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
243 <option value="sbsec">sbsec</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
244 <option value="scanis">scanis</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
245 <option value="schromogenes">schromogenes</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
nml
parents: 14
diff changeset
246 <option value="sdysgalactiae">sdysgalactiae</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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parents: 14
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247 <option value="senterica_achtman_2">senterica_achtman_2</option>
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248 <option value="sepidermidis">sepidermidis</option>
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249 <option value="sgallolyticus">sgallolyticus</option>
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250 <option value="shaemolyticus">shaemolyticus</option>
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251 <option value="shewanella">shewanella</option>
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252 <option value="shominis">shominis</option>
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253 <option value="sinorhizobium">sinorhizobium</option>
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254 <option value="smaltophilia">smaltophilia</option>
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255 <option value="spneumoniae">spneumoniae</option>
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256 <option value="spseudintermedius">spseudintermedius</option>
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257 <option value="spyogenes">spyogenes</option>
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258 <option value="ssuis">ssuis</option>
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259 <option value="staphlugdunensis">staphlugdunensis</option>
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260 <option value="sthermophilus">sthermophilus</option>
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261 <option value="streptomyces">streptomyces</option>
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262 <option value="streptothermophilus">streptothermophilus</option>
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263 <option value="suberis">suberis</option>
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264 <option value="szooepidemicus">szooepidemicus</option>
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265 <option value="taylorella">taylorella</option>
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266 <option value="tenacibaculum">tenacibaculum</option>
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267 <option value="tpallidum">tpallidum</option>
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268 <option value="ureaplasma">ureaplasma</option>
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269 <option value="vcholerae">vcholerae</option>
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270 <option value="vcholerae_2">vcholerae_2</option>
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271 <option value="vibrio">vibrio</option>
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272 <option value="vparahaemolyticus">vparahaemolyticus</option>
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273 <option value="vtapetis">vtapetis</option>
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274 <option value="vvulnificus">vvulnificus</option>
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275 <option value="wolbachia">wolbachia</option>
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276 <option value="xfastidiosa">xfastidiosa</option>
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277 <option value="ypseudotuberculosis_achtman_3">ypseudotuberculosis_achtman_3</option>
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278 <option value="yruckeri">yruckeri</option>
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279 </param>
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280 <conditional name="exclude_genes">
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281 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
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282 <option value="default" selected="true">Exclude default list of AMR genes</option>
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283 <option value="custom">Provide a custom list of AMR genes to exclude</option>
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284 <option value="none">Do not exclude any AMR genes</option>
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285 </param>
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286 <when value="default" />
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287 <when value="custom">
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288 <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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289 </when>
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290 <when value="none" />
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291 </conditional>
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292 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
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293 <option value="include_all" selected="true">Include all available database types</option>
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294 <option value="gram_positive">Gram Positive</option>
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295 <option value="enterobacteriaceae">Enterobacteriaceae</option>
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296 </param>
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297 </section>
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298 </inputs>
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299 <outputs>
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300 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" />
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301 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
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302 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
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303 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
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304 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
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305 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
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306 <filter>pointfinder_db['use_pointfinder'] != "disabled"</filter>
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307 </data>
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308 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
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309 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
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310 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
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311 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
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312 </collection>
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313 </outputs>
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314 <tests>
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315 <test>
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316 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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317 <param name="use_pointfinder" value="salmonella" />
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318
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319 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
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320 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
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321 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
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322 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
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323 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
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324 <output_collection name="blast_hits" type="list">
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325 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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326 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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327 </output_collection>
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328 </test>
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329 <test>
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330 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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331 <param name="use_pointfinder" value="custom" />
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332 <param name="pointfinder_custom" value="escherichia_coli" />
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333
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334 <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" />
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335 <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" />
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336 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
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337 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
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338 <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" />
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339 </test>
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340 <test>
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341 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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342
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343 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
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344 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
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345 <output_collection name="blast_hits" type="list">
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346 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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347 </output_collection>
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348 </test>
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349 <test>
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350 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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351 <section name="advanced">
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352 <param name="mlst_scheme" value="listeria_2" />
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353 </section>
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354 <output name="mlst" file="mlst.tsv" ftype="tabular" />
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355 </test>
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356 <test>
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357 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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358 <param name="pid_threshold" value="99.8" />
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359
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360 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
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361 </test>
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362 <test>
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363 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" />
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364 <param name="pid_threshold" value="99.8" />
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365
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366 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
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367 </test>
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368 <test>
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369 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
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370
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371 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
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372 </test>
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373 <test>
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374 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
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375 <param name="exclude_genes_condition" value="none" />
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376
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377 <output name="summary" file="test6-summary.tsv" ftype="tabular" />
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378 </test>
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379 <test>
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380 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
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381 <param name="exclude_genes_condition" value="custom" />
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382 <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
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383
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384 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
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385 </test>
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386 <test>
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387 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
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388 <param name="genome_size_lower_bound" value="1" />
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389 <param name="genome_size_upper_bound" value="10" />
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390
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391 <output name="summary" file="test8-summary.tsv" ftype="tabular"/>
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392 </test>
0
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393 </tests>
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394 <help><![CDATA[
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395 staramr
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396 =======
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397
6
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398 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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399
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400 Usage
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401 -----
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402
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403 1. Select your genome contigs (in FASTA format).
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404 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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405 3. Run the tool.
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406
4
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407 Input
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408 -----
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409
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410 Genomes
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411 ```````
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412
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413 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.
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414
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415 Exclude genes file
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416 ``````````````````
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417
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418 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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419
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420 ::
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421
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
422 #gene_id
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
423 aac(6')-Iaa_1_NC_003197
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
424 ColpVC_1__JX133088
4
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
nml
parents: 3
diff changeset
425
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
426 Output
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
427 ------
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
428
9
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
429 There are 6 different output files produced by `staramr` as well as a collection of additional files.
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
430
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
431 mlst.tsv
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
432 ````````````````````
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
433
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
434 A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
435
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
436 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
437 | Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 |
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
438 +============+==============+===================================+============+============+============+============+============+============+============+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
439 | SRR1952908 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
440 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
441 | SRR1952926 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
442 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
nml
parents: 8
diff changeset
443
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
444
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
445 summary.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
446 ```````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
447
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
448 A summary of all detected AMR genes/mutations in each genome, one genome per line.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
449
13
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents: 12
diff changeset
450 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
11
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
451 | Isolate ID | Quality Module | Genotype | Predicted Phenotype | Plasmid | Scheme | Sequence Type | Genome Length | N50 value | Number of Contigs Greater Than Or Equal To 300 bp | Quality Module Feedback |
13
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents: 12
diff changeset
452 +============+================+===========================================================+===========================================================================================================+=====================================+===========+===============+===============+===========+===================================================+=========================+
11
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
453 | SRR1952908 | Passed | 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 | senterica | 11 | 4796082 | 225419 | 59 | |
13
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents: 12
diff changeset
454 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
11
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
455 | SRR1952926 | Passed | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11 | 4794071 | 225380 | 50 | |
13
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
nml
parents: 12
diff changeset
456 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
11
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
457
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
458
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
459 detailed_summary.tsv
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
460 ````````````````````
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
461
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
462 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line.
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
463
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
464 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
465 | Isolate ID | Gene/Plasmid | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
466 +============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
467 | SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
468 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
469 | SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
470 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
471 | SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
472 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
473 | SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
474 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
475 | SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
476 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
477 | SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
478 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
479 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
480 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
481 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
482 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
483 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
484 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
485 | SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
486 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
487 | SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
488 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
489 | SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
490 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
491 | SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
492 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
493 | SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
494 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
495 | SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
496 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
497 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
498 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
499 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
500 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
501 | SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
502 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
503
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
504
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
505 resfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
506 `````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
507
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
508 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
509
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
510 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
511 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
512 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
513 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
514 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
515 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
516 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
517 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
518 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
519 | 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
nml
parents:
diff changeset
520 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
521 | 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
nml
parents:
diff changeset
522 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
523 | 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
nml
parents:
diff changeset
524 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
525 | 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
nml
parents:
diff changeset
526 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
527 | 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
nml
parents:
diff changeset
528 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
529
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
530 plasmidfinder.tsv
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
531 `````````````````
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
532
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
533 A tabular file of each AMR plasmid type and additional BLAST information from the **PlasmidFinder** database, one plasmid type per line.
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
534
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
535 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
536 | Isolate ID | Plasmid | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
537 +============+===========+===========+==========+=========================+=============+=======+=======+===========+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
538 | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
539 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
540 | SRR1952908 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
541 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
542 | SRR1952908 | IncFII(S) | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
543 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
544 | SRR1952908 | IncI1 | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
545 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
546 | SRR1952926 | ColpVC | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
547 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
548 | SRR1952926 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
549 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
550 | SRR1952926 | IncFII(S) | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
551 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
552 | SRR1952926 | IncI1 | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
553 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
554
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
555 pointfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
556 ```````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
557
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
558 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
559
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
560 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
561 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
562 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
563 | 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
nml
parents:
diff changeset
564 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
565 | 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
nml
parents:
diff changeset
566 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
567
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
568 settings.txt
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
569 ````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
570
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
571 The command-line, database versions, and other settings used to run `staramr`.
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
572
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
573 ::
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
574
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
575 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
11
5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
nml
parents: 10
diff changeset
576 version = 0.7.1
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
577 start_time = 2019-04-25 16:01:32
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
578 end_time = 2019-04-25 16:01:34
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
579 total_minutes = 0.04
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
580 resfinder_db_dir = staramr/databases/data/dist/resfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
581 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
582 resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
583 resfinder_db_date = Mon, 16 Jul 2018 16:58
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
584 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
585 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
586 pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
587 pointfinder_db_date = Wed, 04 Jul 2018 14:27
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
588 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder
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589 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
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590 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8
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591 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51
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592 pointfinder_gene_drug_version = 050218
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593 resfinder_gene_drug_version = 050218.1
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594
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595 results.xlsx
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596 ````````````
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597
6
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598 An Excel spreadsheet containing the previous 5 files as separate worksheets.
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599
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600 BLAST Hits
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601 ``````````
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602
8
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603 The dataset collection **hits** stores fasta files of the specific blast hits.
0
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604
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605 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
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606
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607 .. _staramr: https://github.com/phac-nml/staramr
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608 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
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609 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
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610 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
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611 .. _webservice: https://cge.food.dtu.dk/services/ResFinder/
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612 ]]></help>
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613 <citations>
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614 <citation type="bibtex">
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615 @Article{microorganisms10020292,
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616 AUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.},
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617 TITLE = {Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr},
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618 JOURNAL = {Microorganisms},
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619 VOLUME = {10},
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620 YEAR = {2022},
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621 NUMBER = {2},
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622 ARTICLE-NUMBER = {292},
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623 URL = {https://www.mdpi.com/2076-2607/10/2/292},
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624 ISSN = {2076-2607},
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625 DOI = {10.3390/microorganisms10020292}
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626 }
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627 </citation>
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628 </citations>
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629 </tool>