Mercurial > repos > nml > staramr

annotate staramr_search.xml @ 10:7573a6c11c4d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
author nml
date Wed, 27 Nov 2019 08:59:23 -0500
parents 61a3e97aa865
children 5f43703968cf
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1 <tool id="staramr_search" name="staramr" version="@VERSION@">
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2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
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3 <macros>
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4 <token name="@VERSION@">0.7.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">staramr</requirement>
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8 </requirements>
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9 <version_command>staramr --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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0
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13 #set $named_genomes = ''
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14 #for $genome in $genomes
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da787fc8b740 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f1641993d71fc04fadf20753a63cc72a412f4af5
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15 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier))
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16 ln -s '$genome' $_named_genome &&
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17 #set $named_genomes = $named_genomes + ' ' + $_named_genome
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18 #end for
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20 #set $excel_proper_extension = '"{}.xlsx"'.format($excel)
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21 ln -s "$excel" $excel_proper_extension &&
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23 staramr search
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25 --nprocs "\${GALAXY_SLOTS:-1}"
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27 --genome-size-lower-bound $advanced.genome_size_lower_bound
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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28 --genome-size-upper-bound $advanced.genome_size_upper_bound
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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29 --minimum-N50-value $advanced.minimum_N50_value
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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30 --minimum-contig-length $advanced.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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31 --unacceptable-number-contigs $advanced.unacceptable_number_contigs
7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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32
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33 --pid-threshold $advanced.pid_threshold
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34 --percent-length-overlap-resfinder $advanced.plength_resfinder
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35 --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder
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36 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
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38 $advanced.report_all_blast
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39 $advanced.exclude_negatives
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40 $advanced.exclude_resistance_phenotypes
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41
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42 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
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43 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
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44 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
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45 --no-exclude-genes
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46 #end if
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47
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48 #if str($advanced.plasmidfinder_type) != 'include_all'
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49 --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
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50 #end if
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51
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52 --output-summary $summary
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53 --output-detailed-summary $detailed_summary
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54 --output-resfinder $resfinder
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55 --output-plasmidfinder $plasmidfinder
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56 #if str($use_pointfinder) != 'disabled'
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57 --output-pointfinder $pointfinder
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58 #end if
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59 --output-settings $settings
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60 --output-excel $excel_proper_extension
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61
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62 --output-hits-dir staramr_hits
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63
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64 #if str($use_pointfinder) != 'disabled'
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65 --pointfinder-organism '${use_pointfinder}'
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66 #end if
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67
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68 $named_genomes
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69 ]]></command>
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70 <inputs>
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71 <param type="data" name="genomes" format="fasta" multiple="true"/>
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72 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
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73 <option value="disabled" selected="true">Disable PointFinder</option>
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74 <option value="salmonella">Salmonella</option>
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75 <option value="campylobacter">Campylobacter</option>
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76 </param>
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77 <section name="advanced" title="Advanced options" expanded="false">
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78 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
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79 min="0" max="100" help="(--pid-threshold)" />
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80 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
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81 min="0" max="100" help="(--percent-length-overlap-resfinder)" />
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82 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
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83 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
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84 <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0"
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85 min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" />
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7573a6c11c4d "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
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86 <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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87 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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88 <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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89 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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90 <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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91 help="(--minimum-N50-value)" />
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92 <param name="minimum_contig_length" type="integer" label="The minimum contig length for the quality metrics" value="300"
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93 help="(--minimum-contig-length)" />
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94 <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"
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95 help="(--unacceptable-number-contigs)" />
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96 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
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97 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
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98 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
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99 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
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100 <conditional name="exclude_genes">
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101 <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results">
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102 <option value="default" selected="true">Exclude default list of AMR genes</option>
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103 <option value="custom">Provide a custom list of AMR genes to exclude</option>
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104 <option value="none">Do not exclude any AMR genes</option>
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105 </param>
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106 <when value="default" />
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107 <when value="custom">
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108 <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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109 </when>
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110 <when value="none" />
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111 </conditional>
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112 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
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113 <option value="include_all" selected="true">Include all available database types</option>
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114 <option value="gram_positive">Gram Positive</option>
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115 <option value="enterobacteriaceae">Enterobacteriaceae</option>
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116 </param>
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117 </section>
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118 </inputs>
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119 <outputs>
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120 <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" />
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121 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
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122 <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
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123 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
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124 <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
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125 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
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126 <filter>use_pointfinder != "disabled"</filter>
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127 </data>
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128 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
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129 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
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130 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
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131 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
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132 </collection>
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133 </outputs>
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134 <tests>
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135 <test>
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136 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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137 <param name="use_pointfinder" value="salmonella" />
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138
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139 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
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140 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
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141 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
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142 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
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143 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
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144 <output_collection name="blast_hits" type="list">
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145 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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146 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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147 </output_collection>
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148 </test>
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149 <test>
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150 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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151
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152 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
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153 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
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154 <output_collection name="blast_hits" type="list">
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155 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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156 </output_collection>
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157 </test>
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158 <test>
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159 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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160 <param name="pid_threshold" value="99.8" />
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161
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162 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
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163 </test>
1
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164 <test>
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165 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
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166 <param name="pid_threshold" value="99.8" />
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167
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168 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
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169 </test>
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170 <test>
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171 <param name="genomes" value="test-aminoglycoside.fsa" />
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172
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173 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
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174 </test>
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175 <test>
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176 <param name="genomes" value="test-aminoglycoside.fsa" />
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177 <param name="exclude_genes_condition" value="none" />
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178
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179 <output name="summary" file="test6-summary.tsv" ftype="tabular" />
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180 </test>
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181 <test>
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182 <param name="genomes" value="test-aminoglycoside.fsa" />
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183 <param name="exclude_genes_condition" value="custom" />
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184 <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
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185
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186 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
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187 </test>
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188 <test>
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189 <param name="genomes" value="test-aminoglycoside.fsa" />
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190 <param name="genome_size_lower_bound" value="1" />
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191 <param name="genome_size_upper_bound" value="10" />
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192
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193 <output name="summary" file="test8-summary.tsv" ftype="tabular"/>
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194 </test>
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195 </tests>
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196 <help><![CDATA[
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197 staramr
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198 =======
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199
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200 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.
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201
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202 Usage
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203 -----
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204
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205 1. Select your genome contigs (in FASTA format).
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206 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* and *campylobacter* is supported).
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207 3. Run the tool.
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208
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209 Input
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210 -----
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211
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212 Genomes
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213 ```````
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214
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215 staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.
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216
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217 Exclude genes file
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218 ``````````````````
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219
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220 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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221
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222 ::
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223
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224 #gene_id
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225 aac(6')-Iaa_1_NC_003197
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226 ColpVC_1__JX133088
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227
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228 Output
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229 ------
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230
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231 There are 6 different output files produced by `staramr` as well as a collection of additional files.
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232
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233 mlst.tsv
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234 ````````````````````
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235
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236 A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.
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237
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238 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
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239 | Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 |
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240 +============+==============+===================================+============+============+============+============+============+============+============+
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241 | SRR1952908 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
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242 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+
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243 | SRR1952926 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
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244 +------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
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245
0
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246
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247 summary.tsv
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248 ```````````
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249
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250 A summary of all detected AMR genes/mutations in each genome, one genome per line.
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251
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252 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
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253 | Isolate ID | Genotype | Predicted Phenotype | Plasmid |
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254 +============+===========================================================+===========================================================================================================+=====================================+
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255 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 |
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256 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
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257 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 |
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258 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
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259
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260 detailed_summary.tsv
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261 ````````````````````
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262
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263 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line.
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264
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265 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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266 | Isolate ID | Gene/Plasmid | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type |
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267 +============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+
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268 | SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid |
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269 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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270 | SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid |
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271 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
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272 | SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
273 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
274 | SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
275 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
276 | SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
277 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
278 | SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
279 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
280 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
281 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
282 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
283 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
284 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
285 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
286 | SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
287 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
288 | SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
289 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
290 | SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
291 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
292 | SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
293 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
294 | SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
295 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
296 | SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
297 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
298 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
299 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
300 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
301 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
nml
parents: 6
diff changeset
302 | SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance |
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
303 +------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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diff changeset
304
0
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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diff changeset
305
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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diff changeset
306 resfinder.tsv
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
diff changeset
307 `````````````
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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diff changeset
308
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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diff changeset
309 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
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diff changeset
310
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
diff changeset
311 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
diff changeset
312 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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parents:
diff changeset
313 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
314 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
315 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
316 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
317 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
318 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
319 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
320 | SRR1952908 | aadA1 | streptomycin | 100.00 | 100.00 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
321 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
322 | SRR1952908 | aadA2 | streptomycin | 99.75 | 100.00 | 792/792 | contig00030 | 7760 | 6969 | JQ364967 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
323 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
324 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
325 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
326 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
327 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
328 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 |
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
nml
parents:
diff changeset
329 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
fef5aff062c7 planemo upload for repository https://github.com/phac-nml/staramr commit 8aafd6d7140b7d8aeb097c80fbb7632397ba5e64
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diff changeset
330
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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diff changeset
331 plasmidfinder.tsv
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
diff changeset
332 `````````````````
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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diff changeset
333
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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diff changeset
334 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
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diff changeset
335
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
diff changeset
336 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
7
f1adc47e017a planemo upload for repository https://github.com/phac-nml/staramr commit dad82f0ddadb5e106a54d5aa6609918325e49d23
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parents: 6
diff changeset
337 | Isolate ID | Plasmid | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
6
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
diff changeset
338 +============+===========+===========+==========+=========================+=============+=======+=======+===========+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
339 | SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
diff changeset
340 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
341 | SRR1952908 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
342 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
343 | SRR1952908 | IncFII(S) | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
diff changeset
344 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
345 | SRR1952908 | IncI1 | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
diff changeset
346 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
347 | SRR1952926 | ColpVC | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
diff changeset
348 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
349 | SRR1952926 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
350 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
351 | SRR1952926 | IncFII(S) | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
diff changeset
352 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
nml
parents: 5
diff changeset
353 | SRR1952926 | IncI1 | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 |
3c09557ac425 planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
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parents: 5
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354 +------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
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355
0
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356 pointfinder.tsv
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357 ```````````````
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358
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359 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
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360
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361 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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362 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End |
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363 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
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364 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 |
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365 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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366 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 |
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367 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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368
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369 settings.txt
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370 ````````````
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371
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372 The command-line, database versions, and other settings used to run `staramr`.
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373
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374 ::
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375
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376 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
9
61a3e97aa865 "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
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377 version = 0.6.1
6
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378 start_time = 2019-04-25 16:01:32
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379 end_time = 2019-04-25 16:01:34
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380 total_minutes = 0.04
0
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381 resfinder_db_dir = staramr/databases/data/dist/resfinder
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382 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
6
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383 resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
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384 resfinder_db_date = Mon, 16 Jul 2018 16:58
0
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385 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
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386 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
6
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387 pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7
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388 pointfinder_db_date = Wed, 04 Jul 2018 14:27
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389 plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder
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390 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
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391 plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8
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392 plasmidfinder_db_date = Tue, 20 Nov 2018 08:51
0
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393 pointfinder_gene_drug_version = 050218
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394 resfinder_gene_drug_version = 050218.1
0
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395
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396 results.xlsx
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397 ````````````
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398
6
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399 An Excel spreadsheet containing the previous 5 files as separate worksheets.
0
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400
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401 BLAST Hits
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402 ``````````
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403
8
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404 The dataset collection **hits** stores fasta files of the specific blast hits.
0
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405
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406 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
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407
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408 .. _staramr: https://github.com/phac-nml/staramr
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409 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
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410 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
0
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411 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
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412 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
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413 ]]></help>
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414 <citations>
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415 <citation type="bibtex">
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416 @misc{githubstaramr,
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417 author = {Petkau, Aaron},
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418 year = {2018},
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419 title = {staramr},
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420 publisher = {GitHub},
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421 journal = {GitHub repository},
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422 url = {https://github.com/phac-nml/staramr},
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423 }</citation>
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424 </citations>
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425 </tool>