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<tool id="computeGC"
      name="computeGC"
      version="1.0.0"
	  profile="16.04">
  <description>computes GC% coverage bias distribution from sample in BAM format. Creates model file for use in NEAT-genReads</description>
  <requirements>
    <requirement type="package" version="2.25.0">bedtools</requirement>
    <requirement type="package">numpy</requirement>
  </requirements>
  <command detect_errors="exit_code">
    <![CDATA[
    bedtools genomecov -d -ibam $bam_file
		#if $in_type.input_type == "built-in":
		  -g ${in_type.reference.fields.path}
		#else:
		  -g ${in_type.reference}
		#end if
		> out.genomecov;
	python2 $__tool_directory__/utilities/computeGC.py
		#if $in_type.input_type == "built-in":
		  -r ${in_type.reference.fields.path}
		#else:
		  -r ${in_type.reference}
		#end if
		-i out.genomecov
		-o $computeGC_modelfile
		-w $windowsize
    ]]>
  </command>
  <inputs>
    <param name="bam_file"
	       type="data"
		   format="bam"
		   label="The BAM file to be used to calculate the GC bias from [-ibam]"
		   help="This will be used by BEDTOOLS to calculate the coverage for each base as preparation by the computeGC tool" 
	/>
	
	<conditional name="in_type">
	  <param name="input_type" type="select" label="Use a built-in FASTA file or one from the history?">
		<option value="built-in">Built-in</option>
		<option value="history">History file</option>
	  </param>
	  <when value="built-in">
		<param name="reference"
			   type="select"
			   label="Select a built-in reference sequence"
			   help="The reference sequence that will be used as the basis for the simulated reads">
		  <options from_data_table="fasta_indexes" />
		</param>
	  </when>
	  <when value="history">
		<param name="reference"
			   type="data"
			   format="fasta"
			   label="The reference sequence (FASTA format)"
			   help="The reference sequence that will be used as the basis for the simulated reads"
		/>
	  </when>
	</conditional>
	
	<param name="windowsize"
		 type="integer"
		 value="10"
		 size="4"
		 min="1"
		 label="Window size"
		 help="Sliding window length [-R]"
	/>
	
  </inputs>
  <outputs>
	<data format="txt"
		  name="computeGC_modelfile"
				label="${bam_file.name.replace('.bam','')}_computeGC.p"
				metadata_source="in_type.reference">
	</data>

  </outputs>
  <tests>
 		<test>
			<param name="bam_file" value="chrMT-PE-VCF-BAM.bam"/>
			<conditional name="in_type">
				<param name="input_type" value="history"/>
			  <param name="reference" value="chrMT.fa" format="fasta"/>
			</conditional>
			<param name="windowsize" value="10"/>
			<output name="computeGC_modelfile" file="chrMT-PE-VCF-BAM-computeGC.p" compare="diff"/>
		</test>

  </tests>
</tool>