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<tool id="computeFraglen"
      name="computeFraglen"
      version="1.0.0"
	  profile="16.04">
  <description>computes empirical fragment length distribution from sample data in BAM format. Creates model file for use in NEAT-genReads</description>
  <requirements>
    <requirement type="package" version="2.7">python</requirement>
    <requirement type="package" version="0.1.19">samtools</requirement>
    <requirement type="package" version="1.9.1">numpy</requirement>
	<requirement type="package">libgfortran</requirement>
  </requirements>
  <command detect_errors="exit_code">
    <![CDATA[
    samtools view -d $bam_file
	| python2 $__tool_directory__/utilities/computeFraglen.py
    ]]>
  </command>
  <inputs>
    <param name="bam_file"
	       type="data"
		   format="bam"
		   label="The BAM file to be used to calculate the fragment from [-]"
		   help="This will be used by SAMTOOLS to convert BAM to SAM as preparation by the computeFraglen tool" 
	/>
			
  </inputs>
  <outputs>
	<data format="txt"
		  name="computeGC_modelfile"
		  from_work_dir="fraglen.p"
		  label="${os.path.splitext($bam_file.name)[0]}_fraglen.p"
		  metadata_source="in_type.reference">
	</data>

  </outputs>
  <tests>
 		<test>
			<param name="bam_file" value="chrMT-PE-VCF-BAM.bam"/>
			<output name="computeGC_modelfile" file="chrMT-PE-VCF-BAM-fraglen.p" compare="diff"/>
		</test>

  </tests>
</tool>