<tool id="pmlst" name="pmlst" version="2.0+galaxy2">
  <description>A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid categorization of IncN plasmids</description>


  <requirements>
    <requirement type="package" version="3.2.0">python3-openid</requirement>
    <requirement type="package" version="21.2.4">pip</requirement>
    <requirement type="package" version="1.79">biopython</requirement>
    <requirement type="package" version="1.5.6">cgecore</requirement>
    <requirement type="package" version="0.8.9">tabulate</requirement>
    <requirement type="package" version="2.7.1">blastn</requirement>
  </requirements>


  <!--<command> python3 $__tool_directory__/pmlst/pmlst.py -i $input -s $s -p $__tool_directory__/pmlst/pmlst_db/ > $output  </command>-->

  <!--<command> perl $__tool_directory__/pmlst.pl $__tool_directory__ $input $s > $output </command>--> 

  <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__/pmlst.pl $__tool_directory__ $_input_file $s > $output



]]></command>

  <inputs>
	  <param format="fasta" name="input" type="data" label="Select FASTA files: " />
	  

	  <param name="s" type="select" label="Scheme database used for pMLST prediction:">

	    <option value="incac">incac</option>
	    <option value="incf">incf</option>
	    <option value="inchi1">inchi1</option>
	    <option value="inchi2">inchi2</option>
	    <option value="inci1">inci1</option>
	    <option value="incn">incn</option>
	    <option value="pbssb1-family">pbssb1-family</option>
	     
          </param>

	   
 </inputs>

 <outputs>	 
    <data format="tabular" name="output" />
 </outputs>

  <help>
  
  </help>
  <citations>
	  <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
	        </citations> 
</tool>