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annotate abricate.xml @ 1:15197951a756 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
author iuc
date Fri, 03 Mar 2017 14:56:09 -0500
parents 862f5a86854d
children 2aa02d2a6af3
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1 <tool id="abricate" name="ABRicate" version="0.3">
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2 <requirements>
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3 <requirement type="package" version="0.3">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 '$fasta_input'
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10 #if $settings.advanced == "advanced"
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11 $settings.no_header
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12 #if str($settings.min_dna_id)
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13 --minid=$settings.min_dna_id
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14 #end if
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15 #if str($settings.cull_limit)
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16 --cull=$settings.cull_limit
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17 #end if
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18 #end if
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19 > '$report'
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20 ]]></command>
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21
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22 <inputs>
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23 <param name="fasta_input" type="data" format="fasta" label="FASTA file" help="To screen for antibiotic resistant genes" />
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24 <conditional name="settings">
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25 <param name="advanced" type="select" label="Specify advanced parameters">
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26 <option value="simple" selected="true">No, use program defaults.</option>
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27 <option value="advanced">Yes, see full parameter list.</option>
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28 </param>
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29 <when value="simple">
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30 </when>
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31 <when value="advanced">
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32 <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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33 <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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34 <param name="cull_limit" argument="--cull" type="integer" value="1" min="0" optional="true" label="Culling limit (encompassing hits)" />
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35 </when>
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36 </conditional>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />
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41 </outputs>
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42
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43 <tests>
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44 <!-- Basic test - will produce no results. -->
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45 <test>
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46 <param name="fasta_input" value="Acetobacter.fna"/>
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47 <param name="advanced" value="simple"/>
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48 <output name="report" ftype="tabular" file="output_noresults.txt" />
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49 </test>
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50
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51 <!-- Basic test - will produce results. -->
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52 <test>
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53 <param name="fasta_input" value="MRSA0252.fna"/>
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54 <param name="advanced" value="simple"/>
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55 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
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56 </test>
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57
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58 <!-- Advanced test - No header. -->
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59 <test>
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60 <param name="fasta_input" value="MRSA0252.fna"/>
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61 <param name="advanced" value="advanced"/>
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62 <param name="no_header" value="True"/>
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63 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
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64 </test>
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65
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66 <!-- Advanced test - Cull limit 100 -->
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67 <test>
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68 <param name="fasta_input" value="MRSA0252.fna"/>
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69 <param name="advanced" value="advanced"/>
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70 <param name="cull_limit" value="100"/>
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71 <output name="report" ftype="tabular" file="output_cull100.txt" compare="contains"/>
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72 </test>
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73
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74 <!-- Advanced test - Min DNA ID 100 -->
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75 <test>
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76 <param name="fasta_input" value="MRSA0252.fna"/>
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77 <param name="advanced" value="advanced"/>
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78 <param name="min_dna_id" value="100"/>
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79 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
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80 </test>
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81 </tests>
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82
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83 <help><![CDATA[
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84 **What it does**
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85
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86 Given a FASTA contig file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The database of these genes is built from ResFinder.
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87
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88 **Output**
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89
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90 ABRicate will produce a tab-seperated output file with the following outputs:
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91
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92 +---------------+------------------------------------------------+
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93 | Column | Description |
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94 +===============+================================================+
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95 | FILE | The filename this hit came from |
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96 +---------------+------------------------------------------------+
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97 | SEQUENCE | The sequence in the filename |
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98 +---------------+------------------------------------------------+
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99 | START | Start coordinate in the sequence |
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100 +---------------+------------------------------------------------+
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101 | END | End coordinate |
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102 +---------------+------------------------------------------------+
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103 | GENE | ABR gene |
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104 +---------------+------------------------------------------------+
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105 | COVERAGE | What proportion of the gene is in our sequence |
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106 +---------------+------------------------------------------------+
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107 | COVERAGE_MAP | A visual represenation |
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108 +---------------+------------------------------------------------+
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109 | GAPS | Was there any gaps in the |
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110 | | alignment - possible pseudogene? |
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111 +---------------+------------------------------------------------+
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112 | %COVERAGE | Proportion of gene covered |
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113 +---------------+------------------------------------------------+
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114 | %IDENTITY | Proportion of exact nucleotide matches |
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115 +---------------+------------------------------------------------+
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116
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117
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118 **Example Output**
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119
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120 ::
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121
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122 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY
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123 Processing: 6008.fna
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124 Found 12 ABR genes in 6008.fna
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125 Klebsiella.fna NC_021232.1 872545 872964 fosA 1-420/420 =============== 0 100.00 100.00
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126 Klebsiella.fna NC_021232.1 1381252 1382427 oqxA 1-1176/1176 =============== 0 100.00 99.32
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127 Klebsiella.fna NC_021232.1 2584899 2585759 blaSHV1 1-861/861 =============== 0 100.00 99.88
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128 ]]></help>
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129
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130 <citations>
1
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131 <citation type="bibtex">
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132 @UNPUBLISHED{Seemann2016,
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133 author = {Seemann, Torsten},
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134 title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
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135 year = {2016},
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136 url = {https://github.com/tseemann/abricate},
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137 }
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138 </citation>
0
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139 </citations>
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140 </tool>