## Set up input files
      
    #import re
    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
    ln -sf '$inputFile' '$escaped_element_identifier' &&
    
      ## Reference sequences

      #set $reference_fasta_filename = "localref.fa"

      
    #if str( $reference_source.reference_source_selector ) == "history":
        ln -sf '${reference_source.ref_file}' '${reference_fasta_filename}' &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if
    

      ## refFlat data
      ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format

      #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
        #if $gene_reference_source.refFlat.ext == 'gff3'
            gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
        #else
            gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
        #end if
        grep -v '^#' refFlat.tab.raw | awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
      #else
        grep -v '^#' ${refFlat} | awk '{if ($3 == "+" || $3 == "-") print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10; else print}' > refFlat.tab &&
      #end if

      ## Start picard command

      
    _JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
    export _JAVA_OPTIONS &&
    
      picard CollectRnaSeqMetrics
      --REF_FLAT refFlat.tab

      #if str( $ribosomal_intervals ) != "None":
          --RIBOSOMAL_INTERVALS '${ribosomal_intervals}'
      #end if

      --STRAND_SPECIFICITY '${strand_specificity}'
      --MINIMUM_LENGTH '${minimum_length}'
      --CHART_OUTPUT '${pdfFile}'

      #for $sequence_to_ignore in $ignore_list:
        --IGNORE_SEQUENCE '${sequence_to_ignore.sequence}'
      #end for

      --RRNA_FRAGMENT_PERCENTAGE '${rrna_fragment_percentage}'
      --METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}'
      --INPUT '$escaped_element_identifier'
      -OUTPUT '${outFile}'
      --REFERENCE_SEQUENCE '${reference_fasta_filename}'
      --ASSUME_SORTED '${assume_sorted}'
      --VALIDATION_STRINGENCY ${validation_stringency}