<tool id="hsp60ecctool/" name="hsp60ECCtool" version="1.1.0">
  <description>allows to get Enterobacter cloacae complex hsp60 cluster from a multi-Fasta file</description>

<requirements>
  <requirement type="package" version="2.12.0">blast</requirement>
  <!--<requirement type="package" version="1.7.2">perl-bioperl</requirement>-->
</requirements>

<command detect_errors="aggressive"><![CDATA[

#import re
        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
            ## Add single quotes around each input file identifier
            #set $_input_file = "'{}'".format($input.element_identifier)
            ln -s '${input}' ${_input_file} &&
            

        perl '$__tool_directory__/hsp60ECCtool.pl' $_input_file $__tool_directory__/database.fasta $ident $output $blast

]]></command>
 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output"  -->
 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->

<inputs>
  <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/>
  <param name="ident" type="text" area="false" value="80.00" label="BLAST percentage identity:" help="percentage identity used in Blast to filter output result" />
</inputs>

 <outputs>
    <data format="tabular" name="output" label="${tool.name}: Result"/>
    <data format="tabular" name="blast" label="${tool.name}: BLAST output" />
 </outputs>

<help><![CDATA[
hsp60ECCtool is a program dedicated to Enterobacter cloacae complex (ECC) that detects and identifies the partial coding sequence of hps60.
It is based on the BLASTn algorithm and a specific dataset (based on sorted hsp60 sequences collected from GenBank ECC assemblies). 
The program helps users to clearly identify the hsp60 cluster and associated members of the Enterobacter cloacae complex. 

- The tested strain(s) must be identified as belonging to the complex by a traditional method (API 20E, mass spectrometry...) before hsp60 typing.
 
- Partial amplification of the gene coding for hsp60 should be performed according to the initiale approach proposed by Hoffmann H. and Roggenkamp A. (2003).

- 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).

- Associated species names are given according to Sutton GG. et al. (2018) and Wu W. et al. (2020).

- 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.
  
This tool is also available using the command line at the KaruBioNet's GitHub page:
https://github.com/karubiotools/hsp60ECCtool
]]>
</help>

<citations>
  <citation type="doi">10.1128/AEM.69.9.5306-5318.2003</citation>
  <citation type="doi">10.3201/eid2408.180151</citation>
  <citation type="doi">10.3389/fmicb.2021.628058</citation>
  <citation type="doi">10.12688/f1000research.14566.2</citation>
  <citation type="doi">10.1128/mSystems.00527-20</citation>
</citations>

</tool>