miRPlant.pl 
   ## Change this to accommodate the number of threads you have available.
        -t \${GALAXY_SLOTS:-4}
	-path \$SCRIPT_PATH

    #for $j, $s in enumerate( $series )
    ##rank_of_series=$j
    -i ${s.input}
    -tag ${s.tag}
    #end for

      ## prepare bowtie index
      #set index_path = ''
      #if str($reference_genome.source) == "history":
          bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
          #set index_path = 'genome'
      #else:
          #set index_path = $reference_genome.index.fields.path
      #end if


   ## Do or not annotate rfam non-miRNA RNAs
    #if $params.annotate_rfam == "yes":

		  ## prepare Rfam bowtie index
		  #set rfam_index_path = ''
		  #if str($params.annotate_rfam.reference_rfam.source) == "history":
			  bowtie-build "$params.annotate_rfam.reference_rfam.own_file" rfam; ln -s "$params.annotate_rfam.reference_rfam.own_file" rfam.fa;
			  #set rfam_index_path = 'rfam'
		  #else:
			  #set rfam_index_path = $params.annotate_rfam.reference_rfam.index.fields.path
		  #end if

		-rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v 
	   ## Do or not delet rfam mapped tags
		#if $params.annotate_rfam.rfamresult.delet_rfam == "yes":
		-D 
		#end if
	#end if


   ## Do or not annotate known microRNAs
    #if $params.known_microRNA == "yes":
	-pre $pre -mat $mat 
	#end if


    -format $format -gfa ${index_path}.fa -idx $index_path -phred $phred   -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe > run.log