--- a/correctGCBias.xml	Tue Sep 17 10:27:29 2013 -0400
+++ b/correctGCBias.xml	Tue Oct 29 17:26:28 2013 -0400
@@ -1,10 +1,9 @@
 <tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.1">
-  <description>uses the output from computeGCBias to generate corrected BAM files</description>
-  <requirements>
-    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
-    <requirement type="package" version="0.1">ucsc_tools</requirement>
-    <requirement type="package" >deepTools</requirement>
-  </requirements>
+    <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())
@@ -18,15 +17,18 @@
 
   correctGCBias
   --bamfile '$temp_bam_path'
-  --species '$species'
   --GCbiasFrequenciesFile $GCbiasFrequenciesFile
-  
-  #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'
@@ -47,28 +49,9 @@
 
   <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."/>
 
-  <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>
+        <expand macro="reference_genome_source" />
+        <expand macro="effectiveGenomeSize" />
 
-  <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 your 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="outFileFormat" type="select" label="File format of the output">
     <option value="bam">bam</option>
     <option value="bw">bigwig</option>
@@ -108,19 +91,16 @@
 
 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
 
-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>