Mercurial > repos > iuc > kleborate
annotate kleborate.xml @ 3:a7c43271312c draft default tip
planemo upload for repository https://github.com/katholt/Kleborate commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201
author | iuc |
---|---|
date | Tue, 31 Oct 2023 16:31:44 +0000 |
parents | 959920e3e800 |
children |
rev | line source |
---|---|
0
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
1 <tool id="kleborate" name="Kleborate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
2 <description>screen genome assemblies of Klebsiella pneumoniae</description> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
3 <macros> |
2
959920e3e800
planemo upload for repository https://github.com/katholt/Kleborate commit 71c5a8dc502eb78404be3735a0d87ea38b62cc83
iuc
parents:
1
diff
changeset
|
4 <token name="@TOOL_VERSION@">2.3.2</token> |
3
a7c43271312c
planemo upload for repository https://github.com/katholt/Kleborate commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201
iuc
parents:
2
diff
changeset
|
5 <token name="@VERSION_SUFFIX@">1</token> |
0
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
6 </macros> |
3
a7c43271312c
planemo upload for repository https://github.com/katholt/Kleborate commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201
iuc
parents:
2
diff
changeset
|
7 <xrefs> |
a7c43271312c
planemo upload for repository https://github.com/katholt/Kleborate commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201
iuc
parents:
2
diff
changeset
|
8 <xref type="bio.tools">kleborate</xref> |
a7c43271312c
planemo upload for repository https://github.com/katholt/Kleborate commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201
iuc
parents:
2
diff
changeset
|
9 </xrefs> |
0
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
10 <requirements> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
11 <requirement type="package" version="@TOOL_VERSION@">kleborate</requirement> |
2
959920e3e800
planemo upload for repository https://github.com/katholt/Kleborate commit 71c5a8dc502eb78404be3735a0d87ea38b62cc83
iuc
parents:
1
diff
changeset
|
12 <requirement type="package" version="2.0.6">kaptive</requirement> |
0
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
13 </requirements> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
14 <version_command>kleborate --version</version_command> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
15 <command detect_errors="aggressive"><![CDATA[ |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
16 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
17 ## Symlink input files for human-readable names in output table |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
18 #for $a in $assemblies |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
19 ln -s '$a' '$a.element_identifier' && |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
20 #end for |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
21 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
22 kleborate |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
23 $resistance |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
24 -o '$outfile' |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
25 #if $kaptive_k |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
26 $kaptive_k |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
27 --kaptive_k_outfile '$kaptive_k_outfile' |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
28 #end if |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
29 #if $kaptive_o |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
30 $kaptive_o |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
31 --kaptive_o_outfile '$kaptive_o_outfile' |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
32 #end if |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
33 #if $min_identity |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
34 --min_identity $min_identity |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
35 #end if |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
36 #if $min_coverage |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
37 --min_coverage $min_coverage |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
38 #end if |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
39 #if $min_spurious_identity |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
40 --min_spurious_identity $min_spurious_identity |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
41 #end if |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
42 #if $min_spurious_coverage |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
43 --min_spurious_coverage $min_spurious_coverage |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
44 #end if |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
45 --assemblies |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
46 #for $a in $assemblies |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
47 '$a.element_identifier' |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
48 #end for |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
49 1> '$concise' |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
50 ]]></command> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
51 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
52 <inputs> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
53 <param argument="--assemblies" type="data" format="fasta" multiple="true" label="FASTA file(s) of assemblies" help="you may provide multiple assemblies for screening"/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
54 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
55 <param argument="--resistance" type="select" label="Turn on resistance genes screening?"> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
56 <option value="">no</option> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
57 <option value="--resistance" selected="true">yes</option> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
58 </param> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
59 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
60 <param argument="--kaptive_k" type="boolean" truevalue="--kaptive_k" falsevalue="" checked="false" label="Turn on screening of K loci?" help="Screen for capsule synthesis loci (K-loci) using the 'Kaptive' tool"/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
61 <param argument="--kaptive_o" type="boolean" truevalue="--kaptive_o" falsevalue="" checked="false" label="Turn on screening of O loci?" help="Screen for lipopolysaccharide loci (O-loci) using the 'Kaptive' tool" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
62 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
63 <param argument="--min_identity" type="integer" min="0" max="100" value="90" label="Minimum alignment percent identity for main results" help="Must be a value between 0 and 100" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
64 <param argument="--min_coverage" type="integer" min="0" max="100" value="80" label="Minimum alignment percent coverage for main results" help="Must be a value between 0 and 100" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
65 <param argument="--min_spurious_identity" type="integer" min="0" max="100" value="80" label="Minimum alignment percent identity for spurious results" help="Must be a value between 0 and 100" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
66 <param argument="--min_spurious_coverage" type="integer" min="0" max="100" value="40" label="Minimum alignment percent coverage for spurious results" help="Must be a value between 0 and 100"/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
67 </inputs> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
68 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
69 <outputs> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
70 <data name="concise" format="tabular" label="${tool.name} on ${on_string}: Concise Results" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
71 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}: Full Results" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
72 <data name="kaptive_k_outfile" format="tabular" label="${tool.name} on ${on_string}: K-loci screening results" > |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
73 <filter>kaptive_k</filter> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
74 </data> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
75 <data name="kaptive_o_outfile" format="tabular" label="${tool.name} on ${on_string}: O-loci screening results" > |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
76 <filter>kaptive_o</filter> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
77 </data> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
78 </outputs> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
79 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
80 <tests> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
81 <test expect_num_outputs="4"><!-- test with resistance, kaptive k and kaptive o outputs --> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
82 <param name="assemblies" value="KP011_S63.scfd.fasta,KP012_S64.scfd.fasta" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
83 <param name="resistance" value="--resistance"/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
84 <param name="kaptive_k" value="--kaptive_k"/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
85 <param name="kaptive_o" value="--kaptive_o"/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
86 <output name="concise" ftype="tabular" file="Kleborate_concise_results.txt" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
87 <output name="outfile" ftype="tabular" file="Kleborate_results.txt" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
88 <output name="kaptive_k_outfile" ftype="tabular" file="Kleborate_kaptive_k_results.txt" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
89 <output name="kaptive_o_outfile" ftype="tabular" file="Kleborate_kaptive_o_results.txt" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
90 </test> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
91 <test expect_num_outputs="2"><!-- test without extra options --> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
92 <param name="assemblies" value="KP011_S63.scfd.fasta,KP012_S64.scfd.fasta" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
93 <param name="resistance" value=""/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
94 <param name="kaptive_k" value=""/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
95 <param name="kaptive_o" value=""/> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
96 <output name="concise" ftype="tabular" file="Kleborate_concise_results_vanilla.txt" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
97 <output name="outfile" ftype="tabular" file="Kleborate_results_vanilla.txt" /> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
98 </test> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
99 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
100 </tests> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
101 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
102 <help><![CDATA[ |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
103 **What it does** |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
104 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
105 Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for: |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
106 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
107 - MLST sequence type |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
108 - species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
109 - ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
110 - virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
111 - antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
112 - K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
113 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
114 For Klebsiella species outside of the KpSC, Kleborate will accurately determine the species and will report the presence of any accessory genes detected (AMR, virulence, K & O types); however species-focused markers (mutational resistance, MLST) and divergent forms of the virulence, K and O loci will not be reported. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
115 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
116 More information can be found on the Kleborate `wiki`_. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
117 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
118 .. _wiki: https://github.com/katholt/Kleborate/wiki |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
119 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
120 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
121 **Outputs** |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
122 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
123 Kleborate outputs the following concise results table (in this example with with resistance and K-loci screening enabled): |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
124 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
125 =============== ===================== ===== =============== ============== ===== ========== ==== ========== ==== =========== ===== =========================== ========= ============ ====== ========== |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
126 strain species ST virulence_score Yersiniabactin YbST Colibactin CbST Aerobactin AbST Salmochelin SmST RmpADC RmST rmpA2 wzi K_locus |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
127 --------------- --------------------- ----- --------------- -------------- ----- ---------- ---- ---------- ---- ----------- ----- --------------------------- --------- ------------ ------ ---------- |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
128 GCF_002248955.1 Klebsiella pneumoniae ST15 0 - 0 - 0 - 0 - 0 - 0 - wzi29 KL106 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
129 GCF_003095495.1 Klebsiella pneumoniae ST258 0 - 0 - 0 - 0 - 0 - 0 - wzi154 KL107 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
130 GCF_000009885.1 Klebsiella pneumoniae ST23 4 ybt 2;ICEKp1 326 - 0 iuc 1 1 iro 1,iro 3 19,18 rmp 3; ICEKp1,rmp 1; KpVP-1 30-1LV,26 rmpA2_3-47% wzi1 KL1 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
131 GCF_900501255.1 Klebsiella pneumoniae ST86 3 - 0 - 0 iuc 1 1 iro 1 1 rmp 1; KpVP-1 26 rmpA2_9*-50% wzi2 KL2 (KL30) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
132 =============== ===================== ===== =============== ============== ===== ========== ==== ========== ==== =========== ===== =========================== ========= ============ ====== ========== |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
133 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
134 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
135 Additional details can be found in the full results table, and the Kaptive screening of K-loci and O-loci each generate additional output tables. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
136 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
137 **Scores** |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
138 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
139 Kleborate outputs a simple categorical virulence score, and if resistance screening is enabled, an antimicrobial resistance score as well. These scores provide a rough categorisation of the strains to facilitate monitoring resistance-virulence convergence. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
140 Virulence score |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
141 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
142 The virulence score ranges from 0 to 5: |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
143 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
144 - 0 = negative for all of yersiniabactin (ybt), colibactin (clb), aerobactin (iuc) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
145 - 1 = yersiniabactin only |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
146 - 2 = yersiniabactin and colibactin (or colibactin only) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
147 - 3 = aerobactin (without yersiniabactin or colibactin) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
148 - 4 = aerobactin with yersiniabactin (without colibactin) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
149 - 5 = yersiniabactin, colibactin and aerobactin |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
150 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
151 Note neither the salmochelin (iro) locus nor rmpADC are explicitly considered in the virulence score, for simplicity. The iro and rmpADC loci typically appear alongside the aerobactin (iuc) locus on the Kp virulence plasmids, and so presence of iuc (score of 3-5) generally implies presence of iro and rmpADC. However we prioritise iuc in the calculation of the score, as aerobactin is specifically associated with growth in blood and is a stronger predictor of the hypervirulence phenotype (see this review). The iro and rmpADC loci are also occasionally present with ybt, in the ICEKp variant - ICEKp1, but this will still score 1. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
152 Resistance score |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
153 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
154 The resistance score ranges from 0 to 3: |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
155 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
156 - 0 = no ESBL, no carbapenemase (regardless of colistin resistance) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
157 - 1 = ESBL, no carbapenemase (regardless of colistin resistance) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
158 - 2 = Carbapenemase without colistin resistance (regardless of ESBL genes or OmpK mutations) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
159 - 3 = Carbapenemase with colistin resistance (regardless of ESBL genes or OmpK mutations) |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
160 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
161 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
162 **Confidence** |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
163 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
164 Kaptive K and O loci screening will indicate the best matching locus and types, and its confidence in the match: |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
165 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
166 - Perfect = the locus was found in a single piece with 100% coverage and 100% identity to the reference. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
167 - Very high = the locus was found in a single piece with ≥99% coverage and ≥95% identity, with no missing genes and no extra genes. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
168 - High = the locus was found in a single piece with ≥99% coverage, with ≤ 3 missing genes and no extra genes. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
169 - Good = the locus was found in a single piece or with ≥95% coverage, with ≤ 3 missing genes and ≤ 1 extra genes. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
170 - Low = the locus was found in a single piece or with ≥90% coverage, with ≤ 3 missing genes and ≤ 2 extra genes. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
171 - None = did not qualify for any of the above. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
172 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
173 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
174 **Spurious hits** |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
175 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
176 The default criteria for detection of virulence and resistance genes targeted for genotyping in Kleborate are minimum nucleotide identity ≥90% and minimum nucleotide sequence coverage ≥80% (these parameters can be changed in the tool settings). |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
177 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
178 To alert users to the possibility that target genes may be missed because of contig breaks or other assembly quality issues, Kleborate will also report the presence of 'spurious' BLAST hits that pass more relaxed criteria (default ≥80% identity, ≥40% coverage), in the dedicated columns spurious_virulence_hits and spurious_resistance_hits. |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
179 ]]></help> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
180 |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
181 <citations> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
182 <citation type="doi">10.1038/s41467-021-24448-3</citation> <!-- Kleborate publication --> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
183 <citation type="doi">10.1099/mgen.0.000102</citation><!-- Kaptive publication --> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
184 </citations> |
383036561810
planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff
changeset
|
185 </tool> |