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planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
author iuc
date Mon, 03 Oct 2016 04:03:20 -0400
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children 3535be5366fc
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1 <tool id="abricate" name="ABRicate" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="0.3">abricate</requirement>
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4 <requirement type="package" version="5.18.1">perl</requirement>
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5 <requirement type="package" version="2.2.31">blast+</requirement>
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6 </requirements>
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7
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8 <version_command>abricate --version</version_command>
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11 abricate "$fasta_input"
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12 #if $settings.advanced == "advanced"
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13 $settings.no_header
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14 #if $settings.min_dna_id
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15 --minid=$settings.min_dna_id
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16 #end if
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17 #if $settings.cull_limit
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18 --cull=$settings.cull_limit
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19 #end if
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20 #end if
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21 > "$report"
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22 ]]></command>
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23
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24 <inputs>
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25 <param name="fasta_input" type="data" format="fasta" label="Select fasta file" help="Specify fasta file to screen for antibiotic resistant genes"/>
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26 <conditional name="settings">
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27 <param name="advanced" type="select" label="Specify advanced parameters">
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28 <option value="simple" selected="true">No, use program defaults.</option>
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29 <option value="advanced">Yes, see full parameter list.</option>
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30 </param>
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31 <when value="simple">
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32 </when>
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33 <when value="advanced">
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34 <param name="no_header" type="boolean" label="Suppress header" truevalue="--noheader" falsevalue=""
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35 help="Suppress output file's column headings" optional="true" />
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36 <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="75" min="0" max="100" help="Minimum DNA identity (default 75, must be between 0-100)" optional="true" />
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37 <param name="cull_limit" type="integer" label="Culling limit" value="1" min="0" help="Culling limit (encompassing hits) (default 1, must be a positive number)" optional="true">
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38 <validator type="in_range" message="This value must be greater than or equal to 0" min="0" max="2147483647"/>
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39 </param>
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40 </when>
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41 </conditional>
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42 </inputs>
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43
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44 <outputs>
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45 <data format="tabular" name="report" label="${tool.name} on ${on_string} report file"/>
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46 </outputs>
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47
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48 <tests>
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49 <!-- Basic test - will produce no results. -->
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50 <test>
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51 <param name="fasta_input" value="Acetobacter.fna"/>
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52 <param name="advanced" value="simple"/>
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53 <output name="report" ftype="tabular" file="output_noresults.txt" />
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54 </test>
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55
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56 <!-- Basic test - will produce results. -->
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57 <test>
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58 <param name="fasta_input" value="MRSA0252.fna"/>
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59 <param name="advanced" value="simple"/>
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60 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
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61 </test>
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62
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63 <!-- Advanced test - No header. -->
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64 <test>
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65 <param name="fasta_input" value="MRSA0252.fna"/>
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66 <param name="advanced" value="advanced"/>
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67 <param name="no_header" value="True"/>
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68 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
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69 </test>
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70
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71 <!-- Advanced test - Cull limit 100 -->
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72 <test>
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73 <param name="fasta_input" value="MRSA0252.fna"/>
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74 <param name="advanced" value="advanced"/>
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75 <param name="cull_limit" value="100"/>
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76 <output name="report" ftype="tabular" file="output_cull100.txt" compare="contains"/>
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77 </test>
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78
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79 <!-- Advanced test - Min DNA ID 100 -->
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80 <test>
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81 <param name="fasta_input" value="MRSA0252.fna"/>
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82 <param name="advanced" value="advanced"/>
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83 <param name="min_dna_id" value="100"/>
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84 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
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85 </test>
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86 </tests>
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87
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88 <help><![CDATA[
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89 **What it does**
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90
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91 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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92
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93 **Output**
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94
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95 ABRicate will produce a tab-seperated output file with the following outputs:
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96
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97 +---------------+------------------------------------------------+
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98 | Column | Description |
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99 +===============+================================================+
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100 | FILE | The filename this hit came from |
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101 +---------------+------------------------------------------------+
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102 | SEQUENCE | The sequence in the filename |
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103 +---------------+------------------------------------------------+
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104 | START | Start coordinate in the sequence |
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105 +---------------+------------------------------------------------+
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106 | END | End coordinate |
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107 +---------------+------------------------------------------------+
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108 | GENE | ABR gene |
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109 +---------------+------------------------------------------------+
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110 | COVERAGE | What proportion of the gene is in our sequence |
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111 +---------------+------------------------------------------------+
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112 | COVERAGE_MAP | A visual represenation |
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113 +---------------+------------------------------------------------+
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114 | GAPS | Was there any gaps in the |
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115 | | alignment - possible pseudogene? |
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116 +---------------+------------------------------------------------+
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117 | %COVERAGE | Proportion of gene covered |
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118 +---------------+------------------------------------------------+
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119 | %IDENTITY | Proportion of exact nucleotide matches |
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120 +---------------+------------------------------------------------+
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121
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122
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123 **Example Output**
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124
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125 ::
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126
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127 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY
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128 Processing: 6008.fna
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129 Found 12 ABR genes in 6008.fna
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130 Klebsiella.fna NC_021232.1 872545 872964 fosA 1-420/420 =============== 0 100.00 100.00
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131 Klebsiella.fna NC_021232.1 1381252 1382427 oqxA 1-1176/1176 =============== 0 100.00 99.32
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132 Klebsiella.fna NC_021232.1 2584899 2585759 blaSHV1 1-861/861 =============== 0 100.00 99.88
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133
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134
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135 ]]></help>
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136
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137 <citations>
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138 <citation type="bibtex">
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139 @UNPUBLISHED{Seemann2016,
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140 author = "Seemann T",
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141 title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
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142 year = "2016",
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143 note = "https://github.com/tseemann/abricate"}
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144 </citation>
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145 </citations>
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146 </tool>