<tool id="PGAP" name="PGAP" version="1.0">
  <description>Pan-Genome Analysis Pipeline </description>
  <requirements>
	 <requirement type="package" version="2.11.0">blast</requirement>
	 <requirement type="package" version="7.480">mafft</requirement>
	 <requirement type="package" version="14.137">mcl</requirement>
	 <requirement type="package" version="3.697">phylip</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')
        #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__}/PGAP_wrapper2.pl -g $input_files -p $proteins -l $named_input_files -o $output >>$logfile 2>&1 	
	]]></command>



  <inputs>
	  <param format="fasta" name="input_files" type="data" multiple="true" label="Coding genes FASTA files"/>
	  <param format="fasta" name="proteins" type="data" multiple="true" label="Protein FASTA files"/>
 </inputs>

 <outputs>
	 <data format="txt" name="output" label="Pangenome presence absence matrix"/>
	 <data format="txt" name="logfile" label="Logfile"/>
</outputs>

</tool>