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annotate abricate.xml @ 3:6e9aea89e388 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 962161e1dde26559d0bc1ce5d7b75d2f354606c5
author iuc
date Mon, 04 Sep 2017 02:47:12 -0400
parents 2aa02d2a6af3
children 78c75f134c16
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1 <tool id="abricate" name="ABRicate" version="0.7">
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2 <requirements>
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3 <requirement type="package" version="0.7">abricate</requirement>
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4 </requirements>
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5
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6 <version_command>abricate --version</version_command>
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7
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8 <command detect_errors="exit_code"><![CDATA[
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9 abricate '$file_input'
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10 $adv.no_header
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11 #if $adv.min_dna_id
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12 --minid=$adv.min_dna_id
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13 #end if
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14 --db=$adv.db
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15 > '$report'
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16 ]]></command>
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17
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18 <inputs>
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19 <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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20 <section name="adv" title="Advanced options" expanded="False">
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21 <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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22 <option value="argannot">argannot</option>
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23 <option value="card">card</option>
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24 <option value="ncbibetalactamase">ncbi betalactamase</option>
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25 <option value="resfinder" selected="true">resfinder</option>
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26 <option value="plasmidfinder">plasmidfinder</option>
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27 <option value="vfdb">vfdb</option>
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28 </param>
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29 <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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30 <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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31 </section>
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32 </inputs>
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33
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34 <outputs>
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35 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />
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36 </outputs>
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37
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38 <tests>
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39 <!-- Basic test 0 - will produce no results. -->
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40 <test>
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41 <param name="file_input" value="Acetobacter.fna"/>
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42 <output name="report" ftype="tabular" file="output_noresults.txt" />
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43 </test>
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44
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45 <!-- Basic test 1 - will produce results. -->
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46 <test>
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47 <param name="file_input" value="MRSA0252.fna"/>
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48 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
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49 </test>
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50
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51 <!-- Advanced test 2 - No header. -->
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52 <test>
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53 <param name="file_input" value="MRSA0252.fna"/>
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54 <param name="no_header" value="True"/>
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55 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
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56 </test>
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57
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58 <!-- Advanced test 3 - Changed DB to card -->
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59 <test>
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60 <param name="file_input" value="MRSA0252.fna"/>
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61 <param name="db" value="card"/>
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62 <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
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63 </test>
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64
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65 <!-- Advanced test 4 - Min DNA ID 100 -->
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66 <test>
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67 <param name="file_input" value="MRSA0252.fna"/>
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68 <param name="min_dna_id" value="100"/>
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69 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
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70 </test>
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71
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72 <!-- Filetype test 5 - input a gbk -->
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73 <test>
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74 <param name="file_input" value="test.gbk"/>
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75 <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
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76 </test>
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77
0
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78 </tests>
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79
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80 <help><![CDATA[
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81 **What it does**
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82
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83 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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84
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85 **Output**
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86
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87 ABRicate will produce a tab-seperated output file with the following outputs:
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88
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89 +---------------+------------------------------------------------+
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90 | Column | Description |
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91 +===============+================================================+
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92 | FILE | The filename this hit came from |
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93 +---------------+------------------------------------------------+
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94 | SEQUENCE | The sequence in the filename |
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95 +---------------+------------------------------------------------+
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96 | START | Start coordinate in the sequence |
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97 +---------------+------------------------------------------------+
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98 | END | End coordinate |
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99 +---------------+------------------------------------------------+
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100 | GENE | ABR gene |
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101 +---------------+------------------------------------------------+
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102 | COVERAGE | What proportion of the gene is in our sequence |
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103 +---------------+------------------------------------------------+
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104 | COVERAGE_MAP | A visual represenation |
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105 +---------------+------------------------------------------------+
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106 | GAPS | Was there any gaps in the |
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107 | | alignment - possible pseudogene? |
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108 +---------------+------------------------------------------------+
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109 | %COVERAGE | Proportion of gene covered |
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110 +---------------+------------------------------------------------+
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111 | %IDENTITY | Proportion of exact nucleotide matches |
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112 +---------------+------------------------------------------------+
2
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113 | DATABASE | The database this sequence comes from |
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114 +---------------+------------------------------------------------+
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115 | ACCESSION | The genomic source of the sequence |
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116 +---------------+------------------------------------------------+
0
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117
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118
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119 **Example Output**
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120
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121 ::
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122
2
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123 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION
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124 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628
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125 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169
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126 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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127 ]]></help>
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128
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129 <citations>
1
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130 <citation type="bibtex">
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131 @UNPUBLISHED{Seemann2016,
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132 author = {Seemann, Torsten},
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133 title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
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134 year = {2016},
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135 url = {https://github.com/tseemann/abricate},
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136 }
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137 </citation>
0
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138 </citations>
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139 </tool>