annotate staramr_search.xml @ 18:3b22de20bd4b draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
author nml
date Tue, 19 Sep 2023 18:41:35 +0000
parents 141afacabcfa
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1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy1" 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@">0.10.0</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
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9 changes depending on the version. I specify the exact version here to make sure
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10 the list of schemes provided is consistent -->
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11 <requirement type="package" version="2.23.0">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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24 #set $excel_proper_extension = 'results.xlsx'
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25 ln -s '$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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31 --genome-size-lower-bound $advanced.genome_size_lower_bound
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32 --genome-size-upper-bound $advanced.genome_size_upper_bound
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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 $advanced.plength_pointfinder
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41
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42 #if str($advanced.mlst_scheme) != 'auto':
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43 --mlst-scheme '${advanced.mlst_scheme}'
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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
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57 #if str($advanced.complex_mutations.complex_mutations_condition) == 'custom'
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58 --complex-mutations-file '${advanced.complex_mutations.complex_mutations_file}'
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59 #end if
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60
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61 #if str($advanced.plasmidfinder_type) != 'include_all'
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62 --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
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63 #end if
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64
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65 --output-summary '$summary'
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66 --output-detailed-summary '$detailed_summary'
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67 --output-resfinder '$resfinder'
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68 --output-plasmidfinder '$plasmidfinder'
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69 --output-settings '$settings'
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70 --output-excel '$excel_proper_extension'
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71 --output-mlst '$mlst'
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72
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73 --output-hits-dir staramr_hits
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74
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75 #if str($pointfinder_db.use_pointfinder) != 'disabled'
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76 --output-pointfinder '$pointfinder'
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77 #if str($pointfinder_db.use_pointfinder) == 'custom'
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78 --pointfinder-organism '${pointfinder_db.pointfinder_custom}'
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79 #else
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80 --pointfinder-organism '${pointfinder_db.use_pointfinder}'
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81 #end if
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82 #end if
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83
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84 $named_genomes
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85 ]]></command>
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86 <inputs>
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87 <param type="data" name="genomes" format="fasta" multiple="true"/>
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88 <conditional name="pointfinder_db">
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89 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
16
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90 <option value="disabled" selected="true">Disable PointFinder</option>
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91 <option value="campylobacter">Campylobacter</option>
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92 <option value="enterococcus_faecalis">enterococcus_faecalis</option>
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93 <option value="enterococcus_faecium">enterococcus_faecium</option>
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94 <option value="escherichia_coli">escherichia_coli</option>
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95 <option value="helicobacter_pylori">helicobacter_pylori</option>
15
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96 <option value="salmonella">Salmonella</option>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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97 <option value="custom">Unvalidated</option>
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98 </param>
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99 <!-- 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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100 <when value="disabled"/>
16
4d83eccf5f81 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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101 <when value="campylobacter"/>
4d83eccf5f81 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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102 <when value="enterococcus_faecalis"/>
4d83eccf5f81 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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parents: 15
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103 <when value="enterococcus_faecium"/>
4d83eccf5f81 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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parents: 15
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104 <when value="escherichia_coli"/>
4d83eccf5f81 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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105 <when value="helicobacter_pylori"/>
15
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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106 <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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107
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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108 <!-- 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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109 <when value="custom">
16
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110 <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.">
15
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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111 <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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112 <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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113 <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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114 <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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115 <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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116 </param>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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117 </when>
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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118 </conditional>
0
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119 <section name="advanced" title="Advanced options" expanded="false">
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120 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
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121 min="0" max="100" help="(--pid-threshold)" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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122 <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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123 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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124 <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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125 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
6
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126 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0"
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127 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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128 <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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129 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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130 <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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131 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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132 <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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133 help="(--minimum-N50-value)" />
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134 <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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135 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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136 <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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137 help="(--unacceptable-number-contigs)" />
0
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138 <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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139 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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140 <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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141 <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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142 <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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143 <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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144 <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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145 <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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146 <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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147 <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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148 <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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149 <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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150 <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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151 <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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152 <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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153 <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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154 <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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155 <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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156 <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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157 <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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158 <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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159 <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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160 <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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161 <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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162 <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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163 <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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164 <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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165 <option value="brucella">brucella</option>
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166 <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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167 <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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168 <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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diff changeset
169 <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
nml
parents: 14
diff changeset
170 <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
nml
parents: 14
diff changeset
171 <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
nml
parents: 14
diff changeset
172 <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
nml
parents: 14
diff changeset
173 <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
nml
parents: 14
diff changeset
174 <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
nml
parents: 14
diff changeset
175 <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
nml
parents: 14
diff changeset
176 <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
177 <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
178 <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
179 <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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <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
186 <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
187 <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
188 <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
189 <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
190 <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
191 <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
192 <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
193 <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
194 <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
195 <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
196 <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
197 <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
198 <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
199 <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
200 <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
201 <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
202 <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
203 <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
204 <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
205 <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
206 <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
207 <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
208 <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
209 <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
210 <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
211 <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
212 <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
213 <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
214 <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
215 <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
216 <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
217 <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
218 <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
219 <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
220 <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
221 <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
222 <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
223 <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
224 <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
225 <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
226 <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
227 <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
228 <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
229 <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
230 <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
231 <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
232 <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
233 <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
234 <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
235 <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
236 <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
237 <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
238 <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
239 <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
240 <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
241 <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
242 <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
243 <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
244 <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
245 <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
246 <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
247 <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
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248 <option value="ranatipestifer">ranatipestifer</option>
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249 <option value="rhodococcus">rhodococcus</option>
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250 <option value="sagalactiae">sagalactiae</option>
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251 <option value="saureus">saureus</option>
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252 <option value="sbsec">sbsec</option>
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253 <option value="scanis">scanis</option>
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254 <option value="schromogenes">schromogenes</option>
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255 <option value="sdysgalactiae">sdysgalactiae</option>
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256 <option value="senterica_achtman_2">senterica_achtman_2</option>
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257 <option value="sepidermidis">sepidermidis</option>
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258 <option value="sgallolyticus">sgallolyticus</option>
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259 <option value="shaemolyticus">shaemolyticus</option>
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260 <option value="shewanella">shewanella</option>
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261 <option value="shominis">shominis</option>
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262 <option value="sinorhizobium">sinorhizobium</option>
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263 <option value="smaltophilia">smaltophilia</option>
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264 <option value="spneumoniae">spneumoniae</option>
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265 <option value="spseudintermedius">spseudintermedius</option>
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266 <option value="spyogenes">spyogenes</option>
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267 <option value="ssuis">ssuis</option>
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268 <option value="staphlugdunensis">staphlugdunensis</option>
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269 <option value="sthermophilus">sthermophilus</option>
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270 <option value="streptomyces">streptomyces</option>
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271 <option value="streptothermophilus">streptothermophilus</option>
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272 <option value="suberis">suberis</option>
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273 <option value="szooepidemicus">szooepidemicus</option>
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274 <option value="taylorella">taylorella</option>
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275 <option value="tenacibaculum">tenacibaculum</option>
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276 <option value="tpallidum">tpallidum</option>
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277 <option value="ureaplasma">ureaplasma</option>
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278 <option value="vcholerae">vcholerae</option>
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279 <option value="vcholerae_2">vcholerae_2</option>
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280 <option value="vibrio">vibrio</option>
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281 <option value="vparahaemolyticus">vparahaemolyticus</option>
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282 <option value="vtapetis">vtapetis</option>
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283 <option value="vvulnificus">vvulnificus</option>
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284 <option value="wolbachia">wolbachia</option>
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285 <option value="xfastidiosa">xfastidiosa</option>
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286 <option value="ypseudotuberculosis_achtman_3">ypseudotuberculosis_achtman_3</option>
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287 <option value="yruckeri">yruckeri</option>
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288 </param>
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289 <conditional name="exclude_genes">
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290 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
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291 <option value="default" selected="true">Exclude default list of AMR genes</option>
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292 <option value="custom">Provide a custom list of AMR genes to exclude</option>
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293 <option value="none">Do not exclude any AMR genes</option>
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294 </param>
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295 <when value="default" />
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296 <when value="custom">
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297 <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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298 </when>
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299 <when value="none" />
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300 </conditional>
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301 <conditional name="complex_mutations">
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302 <param name="complex_mutations_condition" type="select" label="Provide a custom list of complex mutations">
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303 <option value="default" selected="true">Use default list of complex mutations</option>
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304 <option value="custom">Provide a custom list of complex mutations</option>
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305 </param>
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306 <when value="default" />
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307 <when value="custom">
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308 <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" />
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309 </when>
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310 </conditional>
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311 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
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312 <option value="include_all" selected="true">Include all available database types</option>
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313 <option value="gram_positive">Gram Positive</option>
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314 <option value="enterobacteriaceae">Enterobacteriaceae</option>
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315 </param>
0
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316 </section>
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317 </inputs>
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318 <outputs>
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319 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" />
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320 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
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321 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
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322 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
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323 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
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324 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
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325 <filter>pointfinder_db['use_pointfinder'] != "disabled"</filter>
0
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326 </data>
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327 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
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328 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
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329 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
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330 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
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331 </collection>
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332 </outputs>
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333 <tests>
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334 <test expect_num_outputs="9">
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335 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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336 <param name="use_pointfinder" value="salmonella" />
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337
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338 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
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339 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
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340 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
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341 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
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342 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
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343 <output_collection name="blast_hits" type="list">
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344 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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345 <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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346 </output_collection>
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347 </test>
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348 <test expect_num_outputs="9">
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349 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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350 <param name="use_pointfinder" value="escherichia_coli" />
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351
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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352 <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" />
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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353 <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" />
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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354 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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355 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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356 <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" />
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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357 </test>
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358 <test expect_num_outputs="8">
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359 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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360
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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361 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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362 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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363 <output_collection name="blast_hits" type="list">
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364 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
0
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365 </output_collection>
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366 </test>
17
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367 <test expect_num_outputs="8">
15
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368 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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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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369 <section name="advanced">
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370 <param name="mlst_scheme" value="listeria_2" />
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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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371 </section>
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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372 <output name="mlst" file="mlst.tsv" ftype="tabular" />
2fd4d4c9c5c2 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
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373 </test>
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374 <test expect_num_outputs="8">
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375 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
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376 <param name="pid_threshold" value="99.8" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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377
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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378 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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379 </test>
17
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diff changeset
380 <test expect_num_outputs="8">
15
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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381 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" />
1
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382 <param name="pid_threshold" value="99.8" />
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parents: 0
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383
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
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parents: 0
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384 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
3801ea82c888 planemo upload for repository https://github.com/phac-nml/staramr commit 1b3cd6d32c357a59fa437e29ede4a6c1e78427f8
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385 </test>
17
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diff changeset
386 <test expect_num_outputs="8">
15
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387 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
4
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parents: 3
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388
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389 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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390 </test>
17
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391 <test expect_num_outputs="8">
15
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392 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
4
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393 <param name="exclude_genes_condition" value="none" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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394
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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395 <output name="summary" file="test6-summary.tsv" ftype="tabular" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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396 </test>
17
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diff changeset
397 <test expect_num_outputs="8">
15
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parents: 14
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398 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
4
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parents: 3
diff changeset
399 <param name="exclude_genes_condition" value="custom" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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parents: 3
diff changeset
400 <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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401
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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parents: 3
diff changeset
402 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
1e8ec0f861ff planemo upload for repository https://github.com/phac-nml/staramr commit fd6c4338e65d6a33900da6fe7ae6f507105d3446
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parents: 3
diff changeset
403 </test>
17
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parents: 16
diff changeset
404 <test expect_num_outputs="8">
15
be818ae858e4 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3
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parents: 14
diff changeset
405 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
10
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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parents: 9
diff changeset
406 <param name="genome_size_lower_bound" value="1" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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diff changeset
407 <param name="genome_size_upper_bound" value="10" />
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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parents: 9
diff changeset
408
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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409 <output name="summary" file="test8-summary.tsv" ftype="tabular"/>
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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diff changeset
410 </test>
0
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411 </tests>
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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diff changeset
412 <help><![CDATA[
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diff changeset
413 staramr
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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414 =======
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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diff changeset
415
16
4d83eccf5f81 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
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diff changeset
416 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by their respective webservices_) and compiles a summary report of detected antimicrobial resistance genes.
0
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417
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418 Usage
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419 -----
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420
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421 1. Select your genome contigs (in FASTA format).
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422 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.
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423 3. Run the tool.
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424
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425 Input
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426 -----
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427
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428 Genomes
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429 ```````
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430
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431 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.
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432
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433 Exclude genes file
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434 ``````````````````
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435
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436 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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437
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438 ::
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439
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440 #gene_id
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441 aac(6')-Iaa_1_NC_003197
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442 ColpVC_1__JX133088
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443
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444 Complex mutations file
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445 ``````````````````````
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446
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447 Complex mutations describe multiple point mutations that must be simultaneously present in order to confer resistance. Complex mutations may be specified by the user using a TSV-formatted file with the following format:
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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448
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449 ::
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450
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451 positions mandatory phenotype
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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452 mutation(s) mutation(s) phenotype
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453
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454 Where "positions" are all the point mutations to group into the complex mutation (optional and mandatory), "mandatory" are all the point mutations that must be present for the complex mutation to be reported (mandatory is a subset of positions), and phenotype is the phenotype that is conferred when this set of mutations is present.
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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455
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456 Output
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457 ------
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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458
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61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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459 There are 6 different output files produced by `staramr` as well as a collection of additional files.
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460
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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461 mlst.tsv
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462 ````````````````````
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463
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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464 A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.
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465
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466 +------------+---------------------+---------------+---------+---------+---------+---------+---------+---------+----------+
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467 | Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 |
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468 +============+=====================+===============+=========+=========+=========+=========+=========+=========+==========+
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469 | SRR1952908 | senterica_achtman_2 | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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470 | SRR1952926 | senterica_achtman_2 | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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471 +------------+---------------------+---------------+---------+---------+---------+---------+---------+---------+----------+
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472
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473
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474
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475 summary.tsv
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476 ```````````
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477
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478 A summary of all detected AMR genes/mutations in each genome, one genome per line.
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479
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480
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481 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------+---------------------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
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482 | Isolate ID | Quality Module | Genotype | Predicted Phenotype | CGE Predicted Phenotype | Plasmid | Scheme | Sequence Type | Genome Length | N50 value | Number of Contigs Greater Than Or Equal To 300 bp | Quality Module Feedback |
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483 +============+================+===========================================================+===========================================================================================================+===========================================================================================================================================================================================+==============================================+=====================+===============+===============+===========+===================================================+=========================+
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484 | SRR1952908 | Passed | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | Spectinomycin, Streptomycin, Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin, Chloramphenicol, Nalidixic acid, Ciprofloxacin, Sulfamethoxazole, Doxycycline, Tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1-I(Alpha) | senterica_achtman_2 | 11 | 4785500 | 250423 | 41 | |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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485 | SRR1952926 | Passed | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin, Nalidixic acid, Ciprofloxacin, Doxycycline, Tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1-I(Alpha) | senterica_achtman_2 | 11 | 4785451 | 228311 | 40 | |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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486 +------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------+---------------------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
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5f43703968cf "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
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487
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488
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489 detailed_summary.tsv
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490 ````````````````````
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491
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492 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line.
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493
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494 +------------+----------------------------+------------+---------------------+-----------------------------+-----------+----------+-------------------------+-------------+-------+------+-----------+
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495 | Isolate ID | Data | Data Type | Predicted Phenotype | CGE Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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496 +============+============================+============+=====================+=============================+===========+==========+=========================+=============+=======+======+===========+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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497 | SRR1952908 | ST11 (senterica_achtman_2) | MLST | | | | | | | | | |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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498 | SRR1952908 | ColpVC | Plasmid | | | 98.96 | 100.0 | 193/193 | contig00038 | 1618 | 1426 | JX133088 |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
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diff changeset
499 | SRR1952908 | aadA1 | Resistance | streptomycin | Spectinomycin, Streptomycin | 100.0 | 100.0 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
500 +------------+----------------------------+------------+---------------------+-----------------------------+-----------+----------+-------------------------+-------------+-------+------+-----------+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
501
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
502
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
diff changeset
503
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
504 resfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
505 `````````````
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 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
508
18
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
509 +------------+--------+---------------------+---------------------------+-----------+----------+-------------------------+-------------+-------+------+-----------+-----------+-----------+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
510 | Isolate ID | Gene | Predicted Phenotype | CGE Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Sequence | CGE Notes |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
511 +============+========+=====================+===========================+===========+==========+=========================+=============+=======+======+===========+===========+===========+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
512 | SRR1952908 | sul3 | sulfisoxazole | Sulfamethoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | ATGA[...] | |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
513 | SRR1952908 | tet(A) | tetracycline | Doxycycline, Tetracycline | 99.92 | 97.80 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | ATGT[...] | |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
514 +------------+--------+---------------------+---------------------------+-----------+----------+-------------------------+-------------+-------+------+-----------+-----------+-----------+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
515
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
516
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
517 plasmidfinder.tsv
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
518 `````````````````
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
519
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
520 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
521
18
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
522 +------------+-----------+-----------+----------+-------------------------+-------------+-------+------+-----------+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
523 | Isolate ID | Plasmid | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
524 +============+===========+===========+==========+=========================+=============+=======+======+===========+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
525 | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
526 | SRR1952908 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
527 +------------+-----------+-----------+----------+-------------------------+-------------+-------+------+-----------+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
528
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
529
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
530 pointfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
531 ```````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
532
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
533 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
534
18
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
535 +------------+-------------+-----------------------------------+------------------------------+-------+----------+---------------------+-----------+----------+-------------------------+-------------+--------+--------+----------------------+-----------+-----------------------+---------------------+------------------+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
536 | Isolate ID | Gene | Predicted Phenotype | CGE Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Pointfinder Position | CGE Notes | CGE Required Mutation | CGE Mechanism | CGE PMID |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
537 +============+=============+===================================+==============================+=======+==========+=====================+===========+==========+=========================+=============+========+========+======================+===========+=======================+=====================+==================+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
538 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | Nalidixic acid,Ciprofloxacin | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 | S83Y | | | Target modification | 7492118,10471553 |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
539 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | Nalidixic acid,Ciprofloxacin | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 | S83Y | | | Target modification | 7492118,10471553 |
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
540 +------------+-------------+-----------------------------------+------------------------------+-------+----------+---------------------+-----------+----------+-------------------------+-------------+--------+--------+----------------------+-----------+-----------------------+---------------------+------------------+
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
541
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
542
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
543 settings.txt
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
544 ````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
545
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
546 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
547
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
548 ::
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
549
18
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
550 command_line = staramr search --pointfinder-organism enterococcus_faecium -o out pbp5.fa
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
551 version = 0.10.0
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
552 start_time = 2023-08-23 13:37:41
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
553 end_time = 2023-08-23 13:37:42
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
554 total_minutes = 0.02
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
555 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
556 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
18
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
557 resfinder_db_commit = fa32d9a3cf0c12ec70ca4e90c45c0d590ee810bd
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
558 resfinder_db_date = Tue, 24 May 2022 06:51
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
559 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
560 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
18
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
561 pointfinder_db_commit = 8c694b9f336153e6d618b897b3b4930961521eb8
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
562 pointfinder_db_date = Mon, 01 Feb 2021 15:46
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
563 pointfinder_organisms_all = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, plasmodium_falciparum, salmonella, staphylococcus_aureus
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
564 pointfinder_organisms_valid = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
565 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
566 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
18
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
567 plasmidfinder_db_commit = c18e08c17a5988d4f075fc1171636e47546a323d
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
568 plasmidfinder_db_date = Wed, 18 Jan 2023 09:45
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
569 mlst_version = 2.23.0
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
570 pointfinder_organism = enterococcus_faecium
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
571 pointfinder_gene_drug_version = 072621.2
3b22de20bd4b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed
nml
parents: 17
diff changeset
572 resfinder_gene_drug_version = 072621
0
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 results.xlsx
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
575 ````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
576
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
577 An Excel spreadsheet containing the previous 5 files as separate worksheets.
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
578
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
579 BLAST Hits
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
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580 ``````````
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581
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582 The dataset collection **hits** stores fasta files of the specific blast hits.
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583
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584 Galaxy wrapper written by Aaron Petkau and Eric Marinier at the National Microbiology Laboratory, Public Health Agency of Canada.
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585
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586 .. _staramr: https://github.com/phac-nml/staramr
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587 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
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588 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
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589 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
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590 .. _webservices: http://www.genomicepidemiology.org/services/
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591 ]]></help>
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592 <citations>
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593 <citation type="bibtex">
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594 @Article{microorganisms10020292,
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595 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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596 TITLE = {Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr},
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597 JOURNAL = {Microorganisms},
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598 VOLUME = {10},
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599 YEAR = {2022},
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600 NUMBER = {2},
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601 ARTICLE-NUMBER = {292},
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602 URL = {https://www.mdpi.com/2076-2607/10/2/292},
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603 ISSN = {2076-2607},
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604 DOI = {10.3390/microorganisms10020292}
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605 }
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606 </citation>
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607 </citations>
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608 </tool>