Mercurial > repos > iuc > abricate
annotate abricate.xml @ 9:3f3e247c053d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit d436b1a83859581d432639e86ca802b3bfab21bd"
author | iuc |
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date | Tue, 06 Apr 2021 08:54:46 +0000 |
parents | b734db305578 |
children | c2ef298da409 |
rev | line source |
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78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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1 <tool id="abricate" name="ABRicate" version="@VERSION@"> |
78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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2 <description> |
78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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3 Mass screening of contigs for antimicrobial and virulence genes |
78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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4 </description> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
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5 <edam_topics> |
1bb2ba6d3d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
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6 <edam_topic>topic_0622</edam_topic> |
1bb2ba6d3d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
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7 <edam_topic>topic_3301</edam_topic> |
1bb2ba6d3d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
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8 </edam_topics> |
1bb2ba6d3d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
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9 <edam_operations> |
1bb2ba6d3d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
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10 <edam_operation>operation_3482</edam_operation> |
1bb2ba6d3d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
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11 </edam_operations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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12 <macros> |
78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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13 <import>macros.xml</import> |
78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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14 </macros> |
78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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15 <expand macro="requirements" /> |
78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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16 <expand macro="version_command" /> |
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17 |
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18 <command detect_errors="exit_code"><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
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19 #import re |
f9bf6a8d8547
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
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20 #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier) |
f9bf6a8d8547
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
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21 |
f9bf6a8d8547
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
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22 ln -sf '${file_input}' ${sample_name} && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
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23 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
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24 abricate ${sample_name} |
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25 $adv.no_header |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
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26 #if $adv.min_dna_id |
2aa02d2a6af3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
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27 --minid=$adv.min_dna_id |
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28 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
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29 #if $adv.min_cov |
b734db305578
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
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30 --mincov=$adv.min_cov |
b734db305578
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
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31 #end if |
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32 --db=$adv.db |
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33 > '$report' |
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34 ]]></command> |
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35 |
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36 <inputs> |
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37 <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." /> |
2aa02d2a6af3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
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38 <section name="adv" title="Advanced options" expanded="False"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
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39 <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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40 <option value="argannot">ARG-ANNOT</option> |
78c75f134c16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
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41 <option value="card">CARD</option> |
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42 <option value="ecoh">EcOH</option> |
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43 <option value="ncbi">NCBI Bacterial Antimicrobial Resistance Reference Gene Database</option> |
78c75f134c16
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44 <option value="resfinder" selected="true">Resfinder</option> |
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45 <option value="plasmidfinder">PlasmidFinder</option> |
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46 <option value="vfdb">VFDB</option> |
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47 <option value="megares">megares</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
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48 <option value="ecoli_vf">Ecoli_VF</option> |
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49 </param> |
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50 <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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51 <param name="min_dna_id" argument="--minid" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %identity" /> |
b734db305578
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"
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52 <param name="min_cov" argument="--mincov" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %coverage" /> |
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53 </section> |
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54 </inputs> |
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55 |
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56 <outputs> |
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57 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" /> |
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58 </outputs> |
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59 |
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60 <tests> |
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61 <!-- Basic test 0 - will produce no results. --> |
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62 <test> |
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63 <param name="file_input" value="Acetobacter.fna"/> |
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64 <output name="report" ftype="tabular" file="output_noresults.txt" /> |
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65 </test> |
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66 |
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67 <!-- Basic test 1 - will produce results. --> |
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68 <test> |
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69 <param name="file_input" value="MRSA0252.fna"/> |
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70 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/> |
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71 </test> |
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72 |
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73 <!-- Advanced test 2 - No header. --> |
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74 <test> |
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75 <param name="file_input" value="MRSA0252.fna"/> |
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76 <param name="no_header" value="True"/> |
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77 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/> |
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78 </test> |
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79 |
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80 <!-- Advanced test 3 - Changed DB to card --> |
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81 <test> |
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82 <param name="file_input" value="MRSA0252.fna"/> |
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83 <param name="db" value="card"/> |
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84 <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/> |
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85 </test> |
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86 |
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87 <!-- Advanced test 4 - Changed DB to megares --> |
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88 <test> |
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89 <param name="file_input" value="MRSA0252.fna"/> |
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90 <param name="db" value="megares"/> |
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91 <output name="report" ftype="tabular" file="output_db-megares.txt" compare="contains"/> |
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92 </test> |
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93 |
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94 <!-- Advanced test 5 - Min DNA ID 100 --> |
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95 <test> |
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96 <param name="file_input" value="MRSA0252.fna"/> |
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97 <param name="min_dna_id" value="100"/> |
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98 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/> |
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99 </test> |
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100 |
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101 <!-- Advanced test 6 - Min Coverage 100 --> |
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102 <test> |
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103 <param name="file_input" value="MRSA0252.fna"/> |
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104 <param name="min_cov" value="100"/> |
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105 <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/> |
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106 </test> |
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107 |
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108 <!-- Filetype test 7 - input a gbk --> |
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109 <test> |
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110 <param name="file_input" value="test.gbk"/> |
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111 <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/> |
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112 </test> |
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113 |
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114 </tests> |
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115 |
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116 <help><![CDATA[ |
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117 **What it does** |
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118 |
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119 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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120 |
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121 **Output** |
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122 |
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123 ABRicate will produce a tab-seperated output file with the following outputs: |
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124 |
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125 +---------------+------------------------------------------------+ |
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126 | Column | Description | |
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127 +===============+================================================+ |
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128 | FILE | The filename this hit came from | |
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129 +---------------+------------------------------------------------+ |
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130 | SEQUENCE | The sequence in the filename | |
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131 +---------------+------------------------------------------------+ |
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132 | START | Start coordinate in the sequence | |
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133 +---------------+------------------------------------------------+ |
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134 | END | End coordinate | |
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135 +---------------+------------------------------------------------+ |
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136 | GENE | ABR gene | |
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137 +---------------+------------------------------------------------+ |
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138 | COVERAGE | What proportion of the gene is in our sequence | |
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139 +---------------+------------------------------------------------+ |
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140 | COVERAGE_MAP | A visual represenation | |
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141 +---------------+------------------------------------------------+ |
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142 | GAPS | Was there any gaps in the | |
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143 | | alignment - possible pseudogene? | |
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144 +---------------+------------------------------------------------+ |
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145 | %COVERAGE | Proportion of gene covered | |
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146 +---------------+------------------------------------------------+ |
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147 | %IDENTITY | Proportion of exact nucleotide matches | |
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148 +---------------+------------------------------------------------+ |
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149 | DATABASE | The database this sequence comes from | |
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150 +---------------+------------------------------------------------+ |
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151 | ACCESSION | The genomic source of the sequence | |
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152 +---------------+------------------------------------------------+ |
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153 |
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154 |
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155 **Example Output** |
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156 |
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157 :: |
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158 |
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159 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION |
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160 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628 |
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161 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169 |
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162 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832 |
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163 ]]></help> |
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164 |
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165 <expand macro="citations"/> |
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166 </tool> |