preProcess.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

     ## Do or not annotate rfam non-miRNA RNAs
    #if $nocoding.annotate_rfam == "yes":
		  ## prepare Rfam bowtie index
		  #set rfam_index_path = ''
		  #if str($nocoding.reference_rfam.source) == "history":
			  -rfam $nocoding.reference_rfam.own_file 
		  #else:
			  #set rfam_index_path = $nocoding.reference_rfam.index.fields.path
		      -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path
		  #end if
		 -v $nocoding.v
	#end if

        ## prepare bowtie index
        #set index_path = ''
        #if str($reference_genome.source) == "history":
            #set index_path = 'genome'
            -gfa $reference_genome.own_file
		#else:
            #set index_path = $reference_genome.index.fields.path
		   -gfa ${index_path}.fa -idx $index_path
		#end if

    -format $format -phred $phred -a $a -M $mapnt -min $min -max $max -mis $mismatch  > run.log