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annotate abricate.xml @ 5:f9bf6a8d8547 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
author iuc
date Wed, 11 Sep 2019 23:57:17 -0400
parents 78c75f134c16
children 1bb2ba6d3d96
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1 <tool id="abricate" name="ABRicate" version="@VERSION@">
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2 <description>
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3 Mass screening of contigs for antimicrobial and virulence genes
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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13 #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)
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15 ln -sf '${file_input}' ${sample_name} &&
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16
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17 abricate ${sample_name}
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18 $adv.no_header
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19 #if $adv.min_dna_id
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20 --minid=$adv.min_dna_id
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21 #end if
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22 --db=$adv.db
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23 > '$report'
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24 ]]></command>
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25
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26 <inputs>
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27 <param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file." />
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28 <section name="adv" title="Advanced options" expanded="False">
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29 <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
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30 <option value="argannot">ARG-ANNOT</option>
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31 <option value="card">CARD</option>
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32 <option value="ecoh">EcOH</option>
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33 <option value="ncbi">NCBI Bacterial Antimicrobial Resistance Reference Gene Database</option>
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34 <option value="resfinder" selected="true">Resfinder</option>
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35 <option value="plasmidfinder">PlasmidFinder</option>
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36 <option value="vfdb">VFDB</option>
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37 </param>
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38 <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
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39 <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
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40 </section>
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41 </inputs>
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42
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43 <outputs>
1
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44 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />
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45 </outputs>
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46
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47 <tests>
2
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48 <!-- Basic test 0 - will produce no results. -->
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49 <test>
2
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50 <param name="file_input" value="Acetobacter.fna"/>
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51 <output name="report" ftype="tabular" file="output_noresults.txt" />
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52 </test>
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53
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54 <!-- Basic test 1 - will produce results. -->
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55 <test>
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56 <param name="file_input" value="MRSA0252.fna"/>
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57 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
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58 </test>
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59
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60 <!-- Advanced test 2 - No header. -->
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61 <test>
2
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62 <param name="file_input" value="MRSA0252.fna"/>
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63 <param name="no_header" value="True"/>
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64 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
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65 </test>
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66
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67 <!-- Advanced test 3 - Changed DB to card -->
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68 <test>
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69 <param name="file_input" value="MRSA0252.fna"/>
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70 <param name="db" value="card"/>
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71 <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
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72 </test>
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73
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74 <!-- Advanced test 4 - Min DNA ID 100 -->
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75 <test>
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76 <param name="file_input" value="MRSA0252.fna"/>
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77 <param name="min_dna_id" value="100"/>
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78 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
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79 </test>
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81 <!-- Filetype test 5 - input a gbk -->
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82 <test>
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83 <param name="file_input" value="test.gbk"/>
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84 <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
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85 </test>
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86
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87 </tests>
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88
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89 <help><![CDATA[
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90 **What it does**
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91
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92 Given a FASTA contig file or a genbank file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The user can choose which database to search from a list of available AMR databases.
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93
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94 **Output**
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95
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96 ABRicate will produce a tab-seperated output file with the following outputs:
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97
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98 +---------------+------------------------------------------------+
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99 | Column | Description |
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100 +===============+================================================+
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101 | FILE | The filename this hit came from |
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102 +---------------+------------------------------------------------+
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103 | SEQUENCE | The sequence in the filename |
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104 +---------------+------------------------------------------------+
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105 | START | Start coordinate in the sequence |
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106 +---------------+------------------------------------------------+
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107 | END | End coordinate |
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108 +---------------+------------------------------------------------+
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109 | GENE | ABR gene |
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110 +---------------+------------------------------------------------+
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111 | COVERAGE | What proportion of the gene is in our sequence |
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112 +---------------+------------------------------------------------+
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113 | COVERAGE_MAP | A visual represenation |
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114 +---------------+------------------------------------------------+
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115 | GAPS | Was there any gaps in the |
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116 | | alignment - possible pseudogene? |
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117 +---------------+------------------------------------------------+
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118 | %COVERAGE | Proportion of gene covered |
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119 +---------------+------------------------------------------------+
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120 | %IDENTITY | Proportion of exact nucleotide matches |
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121 +---------------+------------------------------------------------+
2
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122 | DATABASE | The database this sequence comes from |
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123 +---------------+------------------------------------------------+
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124 | ACCESSION | The genomic source of the sequence |
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125 +---------------+------------------------------------------------+
0
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126
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127
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128 **Example Output**
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129
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130 ::
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131
2
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132 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION
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133 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628
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134 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169
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135 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832
0
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136 ]]></help>
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137
4
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138 <expand macro="citations"/>
0
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139 </tool>