<tool id="concatenatemultifasta" name="concatenateMultiFasta tool" version="0.1.0">
  <description>allows to concatenate sequences from a multi-Fasta file</description>

<!--<requirements>
  <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__/concatenateMultiFasta.pl' $_input_file > "$output"



]]></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: "/>
</inputs>

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

<help><![CDATA[
concatenateMultiFasta.pl is a Perl script allowing to concatenate/merge multi-Fasta files. Every Fasta sequences contained in one file will be concatenated and the output is a Fasta file containing a unique sequence. 
  
This script belongs to the getSequenceInfo supplementary tools.

- GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools
]]>
</help>

</tool>