annotate abricate.xml @ 6:1bb2ba6d3d96 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
author iuc
date Mon, 07 Oct 2019 14:57:31 -0400
parents f9bf6a8d8547
children b734db305578
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
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
iuc
parents: 3
diff changeset
2 <description>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
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
iuc
parents: 3
diff changeset
4 </description>
6
1bb2ba6d3d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
iuc
parents: 5
diff changeset
5 <edam_topics>
1bb2ba6d3d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
iuc
parents: 5
diff changeset
6 <edam_topic>topic_0622</edam_topic>
1bb2ba6d3d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
iuc
parents: 5
diff changeset
7 <edam_topic>topic_3301</edam_topic>
1bb2ba6d3d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
iuc
parents: 5
diff changeset
8 </edam_topics>
1bb2ba6d3d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
iuc
parents: 5
diff changeset
9 <edam_operations>
1bb2ba6d3d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
iuc
parents: 5
diff changeset
10 <edam_operation>operation_3482</edam_operation>
1bb2ba6d3d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit b769b4cb086cc95f08ddf5da12e17faff3c689cc"
iuc
parents: 5
diff changeset
11 </edam_operations>
4
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
12 <macros>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
13 <import>macros.xml</import>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
14 </macros>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
15 <expand macro="requirements" />
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
16 <expand macro="version_command" />
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
17
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
18 <command detect_errors="exit_code"><![CDATA[
5
f9bf6a8d8547 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
19 #import re
f9bf6a8d8547 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
20 #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)
f9bf6a8d8547 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
21
f9bf6a8d8547 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
22 ln -sf '${file_input}' ${sample_name} &&
f9bf6a8d8547 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
23
f9bf6a8d8547 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
24 abricate ${sample_name}
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
25 $adv.no_header
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
26 #if $adv.min_dna_id
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
27 --minid=$adv.min_dna_id
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
28 #end if
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
29 --db=$adv.db
1
15197951a756 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
30 > '$report'
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
31 ]]></command>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
32
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
33 <inputs>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
34 <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
iuc
parents: 1
diff changeset
35 <section name="adv" title="Advanced options" expanded="False">
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
36 <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
4
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
37 <option value="argannot">ARG-ANNOT</option>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
38 <option value="card">CARD</option>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
39 <option value="ecoh">EcOH</option>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
40 <option value="ncbi">NCBI Bacterial Antimicrobial Resistance Reference Gene Database</option>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
41 <option value="resfinder" selected="true">Resfinder</option>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
42 <option value="plasmidfinder">PlasmidFinder</option>
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
43 <option value="vfdb">VFDB</option>
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
44 </param>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
45 <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
46 <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
47 </section>
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
48 </inputs>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
49
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
50 <outputs>
1
15197951a756 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
51 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
52 </outputs>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
53
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
54 <tests>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
55 <!-- Basic test 0 - will produce no results. -->
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
56 <test>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
57 <param name="file_input" value="Acetobacter.fna"/>
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
58 <output name="report" ftype="tabular" file="output_noresults.txt" />
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
59 </test>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
60
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
61 <!-- Basic test 1 - will produce results. -->
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
62 <test>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
63 <param name="file_input" value="MRSA0252.fna"/>
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
64 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
65 </test>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
66
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
67 <!-- Advanced test 2 - No header. -->
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
68 <test>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
69 <param name="file_input" value="MRSA0252.fna"/>
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
70 <param name="no_header" value="True"/>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
71 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
72 </test>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
73
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
74 <!-- Advanced test 3 - Changed DB to card -->
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
75 <test>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
76 <param name="file_input" value="MRSA0252.fna"/>
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
77 <param name="db" value="card"/>
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
78 <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
79 </test>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
80
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
81 <!-- Advanced test 4 - Min DNA ID 100 -->
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
82 <test>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
83 <param name="file_input" value="MRSA0252.fna"/>
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
84 <param name="min_dna_id" value="100"/>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
85 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
86 </test>
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
87
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
88 <!-- Filetype test 5 - input a gbk -->
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
89 <test>
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
90 <param name="file_input" value="test.gbk"/>
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
91 <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
92 </test>
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
93
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
94 </tests>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
95
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
96 <help><![CDATA[
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
97 **What it does**
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
98
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
99 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.
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
100
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
101 **Output**
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
102
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
103 ABRicate will produce a tab-seperated output file with the following outputs:
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
104
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
105 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
106 | Column | Description |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
107 +===============+================================================+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
108 | FILE | The filename this hit came from |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
109 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
110 | SEQUENCE | The sequence in the filename |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
111 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
112 | START | Start coordinate in the sequence |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
113 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
114 | END | End coordinate |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
115 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
116 | GENE | ABR gene |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
117 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
118 | COVERAGE | What proportion of the gene is in our sequence |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
119 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
120 | COVERAGE_MAP | A visual represenation |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
121 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
122 | GAPS | Was there any gaps in the |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
123 | | alignment - possible pseudogene? |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
124 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
125 | %COVERAGE | Proportion of gene covered |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
126 +---------------+------------------------------------------------+
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
127 | %IDENTITY | Proportion of exact nucleotide matches |
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
128 +---------------+------------------------------------------------+
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
129 | DATABASE | The database this sequence comes from |
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
130 +---------------+------------------------------------------------+
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
131 | ACCESSION | The genomic source of the sequence |
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
132 +---------------+------------------------------------------------+
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
133
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
134
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
135 **Example Output**
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
136
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
137 ::
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
138
2
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
139 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
140 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
141 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169
2aa02d2a6af3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
142 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
143 ]]></help>
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
144
4
78c75f134c16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
145 <expand macro="citations"/>
0
862f5a86854d planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
iuc
parents:
diff changeset
146 </tool>