Mercurial > repos > iuc > abricate

annotate abricate.xml @ 5:c9d4b1376580 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
author iuc
date Wed, 11 Sep 2019 23:56:52 -0400
parents 707050fe53e1
children ce11dd12ec59
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
707050fe53e1 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@">
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
2 <description>
707050fe53e1 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
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
4 </description>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
5 <macros>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
6 <import>macros.xml</import>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
7 </macros>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
8 <expand macro="requirements" />
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
9 <expand macro="version_command" />
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
10
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
5
c9d4b1376580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
12 #import re
c9d4b1376580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
13 #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)
c9d4b1376580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
14
c9d4b1376580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
15 ln -sf '${file_input}' ${sample_name} &&
c9d4b1376580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
16
c9d4b1376580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
iuc
parents: 4
diff changeset
17 abricate ${sample_name}
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
18 $adv.no_header
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
19 #if $adv.min_dna_id
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
20 --minid=$adv.min_dna_id
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
21 #end if
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
22 --db=$adv.db
1
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
23 > '$report'
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
24 ]]></command>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
25
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
26 <inputs>
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
27 <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." />
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
28 <section name="adv" title="Advanced options" expanded="False">
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
29 <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
4
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
30 <option value="argannot">ARG-ANNOT</option>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
31 <option value="card">CARD</option>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
32 <option value="ecoh">EcOH</option>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
33 <option value="ncbi">NCBI Bacterial Antimicrobial Resistance Reference Gene Database</option>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
34 <option value="resfinder" selected="true">Resfinder</option>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
35 <option value="plasmidfinder">PlasmidFinder</option>
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
36 <option value="vfdb">VFDB</option>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
37 </param>
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
38 <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
39 <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
40 </section>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
41 </inputs>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
42
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
43 <outputs>
1
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
44 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
45 </outputs>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
46
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
47 <tests>
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
48 <!-- Basic test 0 - will produce no results. -->
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
49 <test>
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
50 <param name="file_input" value="Acetobacter.fna"/>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
51 <output name="report" ftype="tabular" file="output_noresults.txt" />
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
52 </test>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
53
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
54 <!-- Basic test 1 - will produce results. -->
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
55 <test>
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
56 <param name="file_input" value="MRSA0252.fna"/>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
57 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
58 </test>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
59
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
60 <!-- Advanced test 2 - No header. -->
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
61 <test>
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
62 <param name="file_input" value="MRSA0252.fna"/>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
63 <param name="no_header" value="True"/>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
64 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
65 </test>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
66
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
67 <!-- Advanced test 3 - Changed DB to card -->
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
68 <test>
2
c13e1b424711 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"/>
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
70 <param name="db" value="card"/>
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
71 <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
72 </test>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
73
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
74 <!-- Advanced test 4 - Min DNA ID 100 -->
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
75 <test>
2
c13e1b424711 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"/>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
77 <param name="min_dna_id" value="100"/>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
78 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
79 </test>
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
80
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
81 <!-- Filetype test 5 - input a gbk -->
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
82 <test>
c13e1b424711 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="test.gbk"/>
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
84 <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
85 </test>
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
86
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
87 </tests>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
88
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
89 <help><![CDATA[
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
90 **What it does**
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
91
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
92 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
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
93
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
94 **Output**
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
95
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
96 ABRicate will produce a tab-seperated output file with the following outputs:
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
97
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
98 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
99 | Column | Description |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
100 +===============+================================================+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
101 | FILE | The filename this hit came from |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
102 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
103 | SEQUENCE | The sequence in the filename |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
104 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
105 | START | Start coordinate in the sequence |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
106 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
107 | END | End coordinate |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
108 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
109 | GENE | ABR gene |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
110 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
111 | COVERAGE | What proportion of the gene is in our sequence |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
112 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
113 | COVERAGE_MAP | A visual represenation |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
114 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
115 | GAPS | Was there any gaps in the |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
116 | | alignment - possible pseudogene? |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
117 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
118 | %COVERAGE | Proportion of gene covered |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
119 +---------------+------------------------------------------------+
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
120 | %IDENTITY | Proportion of exact nucleotide matches |
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
121 +---------------+------------------------------------------------+
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
122 | DATABASE | The database this sequence comes from |
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
123 +---------------+------------------------------------------------+
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
124 | ACCESSION | The genomic source of the sequence |
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
125 +---------------+------------------------------------------------+
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
126
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
127
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
128 **Example Output**
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
129
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
130 ::
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
131
2
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
132 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
133 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
134 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169
c13e1b424711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
iuc
parents: 1
diff changeset
135 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
136 ]]></help>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
137
4
707050fe53e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
iuc
parents: 3
diff changeset
138 <expand macro="citations"/>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
139 </tool>