<tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.1">
    <description>uses the output from computeGCBias to generate corrected BAM files</description>
    <expand macro="requirements" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
  <command>
    #import tempfile
    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())

    #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
    #set $temp_bam_path = $temp_bam_handle.name + '.bam'
    #silent $temp_bam_handle.close()
    #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
    #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))


  correctGCBias

    @THREADS@

  --bamfile '$temp_bam_path'
  --GCbiasFrequenciesFile $GCbiasFrequenciesFile

    @reference_genome_source@


  #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
    --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
  #else:
    --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
  #end if


  #if $advancedOpt.showAdvancedOpt == "yes":
    #if str($advancedOpt.region.value) != '':
      --region '$advancedOpt.region'
    #end if
    
    --binSize '$advancedOpt.binSize'  
  #end if
  
  #set newoutFileName="corrected."+str($outFileFormat)
  
  --correctedFile $newoutFileName; mv $newoutFileName $outFileName

  </command>

  <inputs>

  <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />

  <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>

        <expand macro="reference_genome_source" />
        <expand macro="effectiveGenomeSize" />

  <param name="outFileFormat" type="select" label="File format of the output">
    <option value="bam">bam</option>
    <option value="bw">bigwig</option>
    <option value="bg">bedgraph</option>
  </param>
  
  <conditional name="advancedOpt">
    <param name="showAdvancedOpt" type="select" label="Show advanced options" >
        <option value="no" selected="true">no</option>
        <option value="yes">yes</option>
      </param>
      <when value="no" />
      <when value="yes">
          <param name="region" type="text" value=""
            label="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
           
           <param name="binSize" type="integer" value="50" min="1" 
             label="Bin size in bp"
             help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
      </when>
  </conditional>
  </inputs>
  
  <outputs>
    <data format="bam" name="outFileName">
    <change_format>
        <when input="outFileFormat" value="bw" format="bigwig" />
        <when input="outFileFormat" value="bam" format="bam" />
        <when input="outFileFormat" value="bg" format="bedgraph" />
    </change_format>
    </data>
  </outputs>
  <help>

**What it does**

This tool requires the output from computeGCBias to correct the given BAM files according to the method proposed by Benjamini and Speed (2012). Nucleic Acids Res.
The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.

**Output files**:

- GC-normalized BAM file

-----

.. class:: infomark

@REFERENCES@

    </help>
</tool>