Mercurial > repos > iuc > kleborate

annotate kleborate.xml @ 2:03d465ab2322 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/katholt/Kleborate commit 71c5a8dc502eb78404be3735a0d87ea38b62cc83
author iuc
date Mon, 13 Mar 2023 11:39:01 +0000
parents 0c1f4a4565d5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4347265d67cf 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">
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
2 <description>screen genome assemblies of Klebsiella pneumoniae</description>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
3 <macros>
2
03d465ab2322 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>
0
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
6 </macros>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
7 <requirements>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">kleborate</requirement>
2
03d465ab2322 planemo upload for repository https://github.com/katholt/Kleborate commit 71c5a8dc502eb78404be3735a0d87ea38b62cc83
iuc
parents: 1
diff changeset
9 <requirement type="package" version="2.0.6">kaptive</requirement>
0
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
10 </requirements>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
11 <version_command>kleborate --version</version_command>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
12 <command detect_errors="aggressive"><![CDATA[
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
13
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
14 ## Symlink input files for human-readable names in output table
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
15 #for $a in $assemblies
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
16 ln -s '$a' '$a.element_identifier' &&
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
17 #end for
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
18
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
19 kleborate
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
20 $resistance
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
21 -o '$outfile'
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
22 #if $kaptive_k
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
23 $kaptive_k
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
24 --kaptive_k_outfile '$kaptive_k_outfile'
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
25 #end if
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
26 #if $kaptive_o
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
27 $kaptive_o
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
28 --kaptive_o_outfile '$kaptive_o_outfile'
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
29 #end if
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
30 #if $min_identity
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
31 --min_identity $min_identity
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
32 #end if
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
33 #if $min_coverage
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
34 --min_coverage $min_coverage
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
35 #end if
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
36 #if $min_spurious_identity
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
37 --min_spurious_identity $min_spurious_identity
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
38 #end if
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
39 #if $min_spurious_coverage
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
40 --min_spurious_coverage $min_spurious_coverage
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
41 #end if
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
42 --assemblies
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
43 #for $a in $assemblies
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
44 '$a.element_identifier'
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
45 #end for
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
46 1> '$concise'
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
47 ]]></command>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
48
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
49 <inputs>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
50 <param argument="--assemblies" type="data" format="fasta" multiple="true" label="FASTA file(s) of assemblies" help="you may provide multiple assemblies for screening"/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
51
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
52 <param argument="--resistance" type="select" label="Turn on resistance genes screening?">
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
53 <option value="">no</option>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
54 <option value="--resistance" selected="true">yes</option>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
55 </param>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
56
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
57 <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"/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
58 <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" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
59
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
60 <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" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
61 <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" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
62 <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" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
63 <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"/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
64 </inputs>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
65
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
66 <outputs>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
67 <data name="concise" format="tabular" label="${tool.name} on ${on_string}: Concise Results" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
68 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}: Full Results" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
69 <data name="kaptive_k_outfile" format="tabular" label="${tool.name} on ${on_string}: K-loci screening results" >
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
70 <filter>kaptive_k</filter>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
71 </data>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
72 <data name="kaptive_o_outfile" format="tabular" label="${tool.name} on ${on_string}: O-loci screening results" >
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
73 <filter>kaptive_o</filter>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
74 </data>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
75 </outputs>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
76
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
77 <tests>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
78 <test expect_num_outputs="4"><!-- test with resistance, kaptive k and kaptive o outputs -->
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
79 <param name="assemblies" value="KP011_S63.scfd.fasta,KP012_S64.scfd.fasta" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
80 <param name="resistance" value="--resistance"/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
81 <param name="kaptive_k" value="--kaptive_k"/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
82 <param name="kaptive_o" value="--kaptive_o"/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
83 <output name="concise" ftype="tabular" file="Kleborate_concise_results.txt" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
84 <output name="outfile" ftype="tabular" file="Kleborate_results.txt" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
85 <output name="kaptive_k_outfile" ftype="tabular" file="Kleborate_kaptive_k_results.txt" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
86 <output name="kaptive_o_outfile" ftype="tabular" file="Kleborate_kaptive_o_results.txt" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
87 </test>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
88 <test expect_num_outputs="2"><!-- test without extra options -->
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
89 <param name="assemblies" value="KP011_S63.scfd.fasta,KP012_S64.scfd.fasta" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
90 <param name="resistance" value=""/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
91 <param name="kaptive_k" value=""/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
92 <param name="kaptive_o" value=""/>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
93 <output name="concise" ftype="tabular" file="Kleborate_concise_results_vanilla.txt" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
94 <output name="outfile" ftype="tabular" file="Kleborate_results_vanilla.txt" />
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
95 </test>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
96
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
97 </tests>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
98
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
99 <help><![CDATA[
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
100 **What it does**
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
101
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
102 Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
103
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
104 - MLST sequence type
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
105 - species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
106 - ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
107 - virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
108 - antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
109 - K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
110
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
111 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.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
112
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
113 More information can be found on the Kleborate `wiki`_.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
114
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
115 .. _wiki: https://github.com/katholt/Kleborate/wiki
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
116
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
117
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
118 **Outputs**
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
119
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
120 Kleborate outputs the following concise results table (in this example with with resistance and K-loci screening enabled):
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
121
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
122 =============== ===================== ===== =============== ============== ===== ========== ==== ========== ==== =========== ===== =========================== ========= ============ ====== ==========
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
123 strain species ST virulence_score Yersiniabactin YbST Colibactin CbST Aerobactin AbST Salmochelin SmST RmpADC RmST rmpA2 wzi K_locus
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
124 --------------- --------------------- ----- --------------- -------------- ----- ---------- ---- ---------- ---- ----------- ----- --------------------------- --------- ------------ ------ ----------
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
125 GCF_002248955.1 Klebsiella pneumoniae ST15 0 - 0 - 0 - 0 - 0 - 0 - wzi29 KL106
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
126 GCF_003095495.1 Klebsiella pneumoniae ST258 0 - 0 - 0 - 0 - 0 - 0 - wzi154 KL107
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
127 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
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
128 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)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
129 =============== ===================== ===== =============== ============== ===== ========== ==== ========== ==== =========== ===== =========================== ========= ============ ====== ==========
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
130
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
131
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
132 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.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
133
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
134 **Scores**
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
135
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
136 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.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
137 Virulence score
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
138
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
139 The virulence score ranges from 0 to 5:
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
140
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
141 - 0 = negative for all of yersiniabactin (ybt), colibactin (clb), aerobactin (iuc)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
142 - 1 = yersiniabactin only
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
143 - 2 = yersiniabactin and colibactin (or colibactin only)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
144 - 3 = aerobactin (without yersiniabactin or colibactin)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
145 - 4 = aerobactin with yersiniabactin (without colibactin)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
146 - 5 = yersiniabactin, colibactin and aerobactin
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
147
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
148 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.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
149 Resistance score
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
150
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
151 The resistance score ranges from 0 to 3:
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
152
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
153 - 0 = no ESBL, no carbapenemase (regardless of colistin resistance)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
154 - 1 = ESBL, no carbapenemase (regardless of colistin resistance)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
155 - 2 = Carbapenemase without colistin resistance (regardless of ESBL genes or OmpK mutations)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
156 - 3 = Carbapenemase with colistin resistance (regardless of ESBL genes or OmpK mutations)
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
157
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
158
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
159 **Confidence**
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
160
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
161 Kaptive K and O loci screening will indicate the best matching locus and types, and its confidence in the match:
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
162
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
163 - Perfect = the locus was found in a single piece with 100% coverage and 100% identity to the reference.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
164 - Very high = the locus was found in a single piece with ≥99% coverage and ≥95% identity, with no missing genes and no extra genes.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
165 - High = the locus was found in a single piece with ≥99% coverage, with ≤ 3 missing genes and no extra genes.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
166 - Good = the locus was found in a single piece or with ≥95% coverage, with ≤ 3 missing genes and ≤ 1 extra genes.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
167 - Low = the locus was found in a single piece or with ≥90% coverage, with ≤ 3 missing genes and ≤ 2 extra genes.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
168 - None = did not qualify for any of the above.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
169
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
170
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
171 **Spurious hits**
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
172
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
173 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).
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
174
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
175 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.
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
176 ]]></help>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
177
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
178 <citations>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
179 <citation type="doi">10.1038/s41467-021-24448-3</citation> <!-- Kleborate publication -->
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
180 <citation type="doi">10.1099/mgen.0.000102</citation><!-- Kaptive publication -->
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
181 </citations>
4347265d67cf planemo upload for repository https://github.com/katholt/Kleborate commit 7a486326f6d0ca87c1c41e857732319d31372799
iuc
parents:
diff changeset
182 </tool>