--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/correctGCBias.xml	Thu Nov 14 16:39:18 2013 -0500
@@ -0,0 +1,106 @@
+<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), $temp_bam_path))
+
+
+  correctGCBias
+  --bamfile '$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="Input 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>