diff correctGCBias.xml @ 24:d7c9fd76e41e draft

Uploaded

--- a/correctGCBias.xml	Tue Feb 04 03:38:20 2014 -0500
+++ b/correctGCBias.xml	Tue Feb 04 09:12:07 2014 -0500
@@ -45,7 +45,7 @@
         ##--correctedFile $newoutFileName;
         --correctedFile "corrected.bam";
 
-        mv $newoutFileName $outFileName
+        mv "corrected.bam" $outFileName
     </command>
     <inputs>
         <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
@@ -88,13 +88,11 @@
 
 **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.
-
+This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by
+Benjamini and Speed (2012) Nucleic Acids Res.
+The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
 
-You can find more details in the `correctGCBias wiki`_.
-
-.. _correctGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
+You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
 
 
 **Output files**: