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estrain@6
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1 <tool id="amrfinder" name="amrfinder-plus" version="@VERSION@+galaxy1">
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estrain@6
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2 <description>
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estrain@6
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3 identifies AMR genes using either protein annotations or nucleotide sequence.
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estrain@6
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4 </description>
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estrain@6
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5 <macros>
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estrain@6
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6 <token name="@VERSION@">3.8.4</token>
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estrain@6
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7 </macros>
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estrain@6
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8 <requirements>
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9 <requirement type="package" version="@VERSION@">ncbi-amrfinderplus</requirement>
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estrain@6
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10 </requirements>
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estrain@6
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11 <version_command><![CDATA[amrfinder --version]]></version_command>
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12
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13 <command detect_errors="exit_code"><![CDATA[
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14 amrfinder
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estrain@6
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15 $plus
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16 --threads \${GALAXY_SLOTS:-1}
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17 --database '$amrfinder_databases.fields.path'
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estrain@6
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18 #if $input_selection.input_source_selector == 'nuc'
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19 -n '$input_selection.fasta_file'
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estrain@6
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20 #elif $input_selection.input_source_selector == 'pro'
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21 -p '$input_selection.fasta_file'
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estrain@6
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22 #if $input_selection.gff.use == 'gff_yes'
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23 -g '$input_selection.gff.gff_file'
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estrain@6
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24 #end if
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estrain@6
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25 #elif $input_selection.input_source_selector == 'both'
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estrain@6
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26 -n '$input_selection.nuc_file'
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estrain@6
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27 -p '$input_selection.pro_file'
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estrain@6
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28 #if $input_selection.gff.use == 'gff_yes'
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estrain@6
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29 -g '$input_selection.gff.gff_file'
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estrain@6
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30 #end if
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estrain@6
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31 #end if
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estrain@6
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32 #if str($organism) != 'None'
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estrain@6
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33 -O $organism
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estrain@6
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34 #end if
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35 -o results.tsv
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36 $report_common
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37 #if $point_mut_all
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38 --point_mut_all point_mutate.tsv
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39 #end if
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estrain@6
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40 $gpipe
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41 ]]> </command>
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42
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43 <inputs>
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44 <conditional name="input_selection">
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45 <param name="input_source_selector" type="select" label="Input data type">
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46 <option value="nuc">Nucleotide</option>
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47 <option value="pro">Protein</option>
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estrain@6
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48 <option value="both">Nucleotide and Protein</option>
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49 </param>
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estrain@6
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50 <when value="nuc">
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51 <param name="fasta_file" type="data" format="fasta" label="Select nucleotide fasta file"/>
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estrain@6
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52 </when>
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53 <when value="pro">
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54 <param name="fasta_file" type="data" format="fasta" label="Select protein fasta file"/>
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estrain@6
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55 <conditional name="gff">
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56 <param name="use" type="select" label="Using GFF to get genomic coordinates">
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57 <option value="gff_yes">Yes</option>
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58 <option value="gff_no" selected="true">No</option>
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59 </param>
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estrain@6
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60 <when value="gff_yes">
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61 <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/>
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estrain@6
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62 </when>
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estrain@6
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63 <when value="gff_no">
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64 </when>
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estrain@6
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65 </conditional>
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estrain@6
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66 </when>
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estrain@6
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67 <when value="both">
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estrain@6
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68 <param name="nuc_file" type="data" format="fasta" label="Select a nucleotide fasta file"/>
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estrain@6
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69 <param name="pro_file" type="data" format="fasta" label="Select a protein fasta file"/>
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estrain@6
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70 <conditional name="gff">
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estrain@6
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71 <param name="use" type="select" label="Using GFF to get genomic coordinates">
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72 <option value="gff_yes">Yes</option>
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73 <option value="gff_no" selected="true">No</option>
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estrain@6
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74 </param>
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estrain@6
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75 <when value="gff_yes">
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estrain@6
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76 <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/>
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estrain@6
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77 </when>
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estrain@6
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78 <when value="gff_no">
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79 </when>
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estrain@6
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80 </conditional>
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81 </when>
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82 </conditional>
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estrain@6
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83 <!-- DATABASE INPUT-->
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84 <param name="amrfinder_databases" label="Select a database" type="select">
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85 <options from_data_table="amrfinder_databases">
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86 <validator message="No database is available" type="no_options" />
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87 </options>
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estrain@6
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88 </param>
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89 <param name="organism" type="select" optional="true" label="Get organism-specific results">
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90 <option value="Campylobacter">Campylobacter</option>
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91 <option value="Escherichia">Escherichia</option>
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92 <option value="Klebsiella">Klebsiella</option>
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93 <option value="Salmonella">Salmonella</option>
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94 <option value="Staphylococcus">Staphylococcus</option>
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95 <option value="Vibrio">Vibrio</option>
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96 </param>
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97 <param name="min_iden" argument="--ident_min" type="float" value="-1" label="Minimum identity for a blast-based hit" help="(Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs" />
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98 <param name="min_cov" argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage of the reference protein" />
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99 <param name="plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report" />
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100 <param name="report_common" type="boolean" truevalue="--report_common" falsevalue="" label="Suppress proteins common to a taxonomy group" />
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101 <param name="point_mut_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of reference point mutations" />
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102 <param name="gpipe" type="boolean" truevalue="--gpipe" falsevalue="" label="Protein identifiers in the protein FASTA file have format gnl-project-accession" />
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103 </inputs>
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104
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105 <outputs>
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106 <data name="result" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Result"/>
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107 <data name="point_mutate" format="tabular" from_work_dir="point_mutate.tsv" label="${tool.name} on ${on_string}: Point mutate all">
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estrain@6
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108 <filter>point_mut_all</filter>
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109 </data>
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110 </outputs>
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111
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112 <tests>
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113 <test> <!-- dna input-->
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114 <param name="input_source_selector" value="nuc"/>
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115 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
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116 <param name="amrfinder_databases" value="2019-08-27.1" />
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117 <output name="result" file="test_dna.expected" lines_diff="1"/>
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118 </test>
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estrain@6
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119 <test> <!-- dna input and organism, plus gene-->
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estrain@6
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120 <param name="input_source_selector" value="nuc"/>
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estrain@6
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121 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
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122 <param name="organism" value="Escherichia" />
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123 <param name="plus" value="true" />
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124 <param name="amrfinder_databases" value="2019-08-27.1" />
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125 <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/>
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126 </test>
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estrain@6
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127 <test> <!-- AA input-->
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128 <param name="input_source_selector" value="pro"/>
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129 <param name="fasta_file" value="test_prot.fa" ftype="fasta"/>
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estrain@6
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130 <param name="amrfinder_databases" value="2019-08-27.1" />
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131 <output name="result" file="test_prot.expected" lines_diff="1"/>
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132 </test>
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estrain@6
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133 <test> <!-- DNA and AA input-->
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134 <param name="input_source_selector" value="both"/>
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135 <param name="use" value="gff_yes"/>
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estrain@6
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136 <param name="nuc_file" value="test_dna.fa" ftype="fasta"/>
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137 <param name="pro_file" value="test_prot.fa" ftype="fasta"/>
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138 <param name="use" value="gff_yes"/>
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139 <param name="gff_file" value="test_prot.gff" ftype="gff3"/>
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140 <param name="amrfinder_databases" value="2019-08-27.1" />
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141 <output name="result" file="test_both.expected" lines_diff="1"/>
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142 </test>
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143 </tests>
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144
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145
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146 <help><![CDATA[
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147 This software and the accompanying database are designed to find acquired
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148 antimicrobial resistance genes in bacterial protein or assembled nucleotide
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149 sequences as well as known point mutations for several taxa. With
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150 AMRFinderPlus we have added select members of additional classes of genes
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151 such as virulence factors, biocide, heat, acid, and metal resistance genes.
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152 More details: https://github.com/ncbi/amr/wiki
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153 ]]> </help>
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154 <citations>
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155 <citation type="doi">10.1101/550707</citation>
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156 </citations>
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157
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158 </tool>
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