|
0
|
1 <tool id="hsp60ecctool/" name="hsp60ECCtool" version="1.1.0">
|
|
|
2 <description>allows to get Enterobacter cloacae complex hsp60 cluster from a multi-Fasta file</description>
|
|
|
3
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2.12.0">blast</requirement>
|
|
|
6 <!--<requirement type="package" version="1.7.2">perl-bioperl</requirement>-->
|
|
|
7 </requirements>
|
|
|
8
|
|
|
9 <command detect_errors="aggressive"><![CDATA[
|
|
|
10
|
|
|
11 #import re
|
|
|
12 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
|
|
|
13 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
|
|
|
14 ## Add single quotes around each input file identifier
|
|
|
15 #set $_input_file = "'{}'".format($input.element_identifier)
|
|
|
16 ln -s '${input}' ${_input_file} &&
|
|
|
17
|
|
|
18
|
|
|
19 perl '$__tool_directory__/hsp60ECCtool.pl' $_input_file $__tool_directory__/database.fasta $ident $output $blast
|
|
|
20
|
|
|
21 ]]></command>
|
|
|
22 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" -->
|
|
|
23 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
|
|
|
24
|
|
|
25 <inputs>
|
|
|
26 <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/>
|
|
|
27 <param name="ident" type="text" area="false" value="80.00" label="BLAST percentage identity:" help="percentage identity used in Blast to filter output result" />
|
|
|
28 </inputs>
|
|
|
29
|
|
|
30 <outputs>
|
|
|
31 <data format="tabular" name="output" label="${tool.name}: Result"/>
|
|
|
32 <data format="tabular" name="blast" label="${tool.name}: BLAST output" />
|
|
|
33 </outputs>
|
|
|
34
|
|
|
35 <help><![CDATA[
|
|
|
36 hsp60ECCtool is a program dedicated to Enterobacter cloacae complex (ECC) that detects and identifies the partial coding sequence of hps60.
|
|
|
37 It is based on the BLASTn algorithm and a specific dataset (based on sorted hsp60 sequences collected from GenBank ECC assemblies).
|
|
|
38 The program helps users to clearly identify the hsp60 cluster and associated members of the Enterobacter cloacae complex.
|
|
|
39
|
|
|
40 - The tested strain(s) must be identified as belonging to the complex by a traditional method (API 20E, mass spectrometry...) before hsp60 typing.
|
|
|
41
|
|
|
42 - Partial amplification of the gene coding for hsp60 should be performed according to the initiale approach proposed by Hoffmann H. and Roggenkamp A. (2003).
|
|
|
43
|
|
|
44 - Hsp60 cluster assignment was done according to the original research article and additional analysis provided by Berouthy R. et al. (2018) and Pot M. et al. (2021).
|
|
|
45
|
|
|
46 - Associated species names are given according to Sutton GG. et al. (2018) and Wu W. et al. (2020).
|
|
|
47
|
|
|
48 - Best results are given in the hsp60ECCtool Result output. UD : Undefined Cluster (see in Figure S1 in the supplementary material provided by Pot M. et al. (2020)); NA : Not Attributed in the related research paper. Without whole-genome sequencing and additional analyses, the precise species identification remains indicative and should be taken with caution.
|
|
|
49
|
|
|
50 This tool is also available using the command line at the KaruBioNet's GitHub page:
|
|
|
51 https://github.com/karubiotools/hsp60ECCtool
|
|
|
52 ]]>
|
|
|
53 </help>
|
|
|
54
|
|
|
55 <citations>
|
|
|
56 <citation type="doi">10.1128/AEM.69.9.5306-5318.2003</citation>
|
|
|
57 <citation type="doi">10.3201/eid2408.180151</citation>
|
|
|
58 <citation type="doi">10.3389/fmicb.2021.628058</citation>
|
|
|
59 <citation type="doi">10.12688/f1000research.14566.2</citation>
|
|
|
60 <citation type="doi">10.1128/mSystems.00527-20</citation>
|
|
|
61 </citations>
|
|
|
62
|
|
|
63 </tool>
|
|
|
64
|
