<tool id="catchsequence" name="Catch Sequence" version="0.1.0">
  <description>Catch sequence for BioloMICS import</description>
<requirements>
  <requirement type="package" version="1.0.1">abricate</requirement>
  <requirement type="package" version="2.19.0">mlst</requirement>
  <!--<requirement type="package" version="6.6.0">emboss</requirement>
  <requirement type="package" version="1.3.2">pandas</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')
        #set $named_input_files = ''
        #for $input_file in $input_files
            ## Add single quotes around each input file identifier
            #set $_input_file = "'{}'".format($input_file.element_identifier)
            ln -s '${input_file}' ${_input_file} && 
            #set $named_input_files = $named_input_files + ' ' + $_input_file
        #end for

	
  	perl '$__tool_directory__/catchsequence.pl' $named_input_files > "$output"
	
       

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

<inputs>
  <param type="data" name="input_files" format="fasta" multiple="true" label="Genome fasta files"/>
  <!-- <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> -->
</inputs>

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

<help>
No documentation
  </help>

</tool>