--- a/computeGCBias.xml	Tue Sep 17 10:27:29 2013 -0400
+++ b/computeGCBias.xml	Tue Oct 29 17:26:28 2013 -0400
@@ -1,16 +1,15 @@
 <tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.1">
-  <description>to see whether your samples should be normalized for GC bias</description>
-  
-  <requirements>
-    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
-    <requirement type="package" >deepTools</requirement>
-  </requirements>
-  <stdio>
-    <exit_code range="0" level="warning" description="Warning" />
-  </stdio>
-  <command>
-    #import tempfile
-    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+    <description>to see whether your samples should be normalized for GC bias</description>
+    <expand macro="requirements" />
+    <stdio>
+        <exit_code range="0" level="warning" description="Warning" />
+    </stdio>
+    <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'
@@ -20,26 +19,27 @@
 
   computeGCBias
 
-  ##ToDo
-  --numberOfProcessors 4
+    @THREADS@
 
   --bamfile '$temp_bam_path'
-  --species '$species'
   --GCbiasFrequenciesFile $outFileName
   --fragmentLength $fragmentLength
 
-  #if $source.ref_source=="history":
-    --genome $source.input1
+    @reference_genome_source@
+
+
+  #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+    --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
   #else:
-    --genome "${source.input1_2bit.fields.path}"
+    --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
   #end if
 
+
   #if $advancedOpt.showAdvancedOpt == "yes":
     #if str($advancedOpt.region.value) != '':
       --region '$advancedOpt.region'
     #end if
     
-    --binSize '$advancedOpt.binSize'
     --sampleSize '$advancedOpt.sampleSize'
     --regionSize '$advancedOpt.regionSize'
 
@@ -66,34 +66,15 @@
 
   ; rm $temp_dir -rf
 
-  </command>
-  <inputs>
-
-      <param name="bamInput" format="bam" type="data" label="Input BAM file"
-        help="The BAM file must be sorted."/>
-      <!--<param name="species" type="text" value="" label="Species name abbreviation" />-->
-
-        <param name="species" type="select" label="Species name abbreviation">
-            <option value="hg19">hg19</option>
-            <option value="ce10">ce10</option>
-            <option value="dm3">dm3</option>
-            <option value="mm9">mm9</option>
-        </param>
+    </command>
+    <inputs>
 
-      <conditional name="source">
-        <param name="ref_source" type="select" label="Reference genome">
-            <option value="cached">locally cached</option>
-            <option value="history">in your history</option>
-        </param>
-        <when value="cached">
-            <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-                <options from_data_table="deepTools_seqs" />
-            </param>
-        </when>
-        <when value="history">
-            <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
-        </when>
-      </conditional>
+        <param name="bamInput" format="bam" type="data" label="Input BAM file"
+            help="The BAM file must be sorted."/>
+
+        <expand macro="reference_genome_source" />
+        <expand macro="effectiveGenomeSize" />
+
       <param name="fragmentLength" type="integer" value="300" min="1"
         label="Fragment length used for the sequencing"
         help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
@@ -108,10 +89,6 @@
           <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."/>
              
            <param name="sampleSize" type="integer" value="50000000" min="1"
              label="Number of sampling points to be considered" />
@@ -171,16 +148,26 @@
 In an ideal sample without GC bias, the ratio of OBSERVED/EXPECTED values should be close to 1 regardless of the GC content. Due to PCR (over)amplifications, the majority of ChIP samples
 usually shows a significant bias towards reads with high GC content (>50%)
 
+.. image:: $PATH_TO_IMAGES/QC_GCplots_input.png
+
+
+**Output files**:
+
+- Diagnostic plot
+
+  - box plot of absolute read numbers per genomic GC bin
+  - x-y plot of observed/expected read ratios per genomic GC content bin
+
+- Data matrix
+
+  - to be used for GC correction with correctGCbias
+
+
 -----
 
 .. class:: infomark
 
-If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
-
-This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+@REFERENCES@
 
-.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
-.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-
-  </help>
+    </help>
 </tool>