siRNA_pipeline.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


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



   ## Do or not annotate siRNAs by function
    #if $params.function_anno == "yes":
     -nat $params.nat -repeat $params.repeat
	#end if
   
   ## Do or not DEG
    #if $degseq.degseq_analysis == "yes" :
    -deg $degseq.deg
    #end if

  -format $format -phred $phred -g ${index_path}.fa -idx $index_path -f $gff -mis $mis -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v -a $a -n $mapnt -d $d -p $p -l $l  -cen $cen -span $span > run.log