<tool id="repeat_element_identifier" name="repeat_element_identifier" version="0.0.1" hidden="false" >
  <description>Analyze mismatch frequencies in BAM/SAM alignments</description>
  <requirements>
  </requirements>
  <command>>
		#for i in $rep
			echo "$i.input_file.element_identifier" > "$output"
		#end for
  </command>
  <inputs>
    <repeat name="rep" title="input">
      <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which to analyze the mismatches."/>
    </repeat>
  </inputs>
  <outputs>
    <data name="output" />
  </outputs>
  <tests>
  </tests>
  <help>
This tool will print the element identifier of files in a repeat section.
  </help>
  <citations>
  </citations>
</tool>