# HG changeset patch
# User bgruening
# Date 1391252698 18000
# Node ID 2f7edf06a5da41e72de4674653c2e735602aafa1
# Parent  ea2f64efe70dec03d2a0fdda28b587bf93d2981a
Uploaded

diff -r ea2f64efe70d -r 2f7edf06a5da bamCompare.xml
--- a/bamCompare.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/bamCompare.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -37,7 +37,13 @@
           #if $comparison.normalization.type=='rpkm':
             --normalizeUsingRPKM
           #elif $comparison.normalization.type=='1x':
-            --normalizeTo1x $comparison.normalization.normalizeTo1x
+
+            #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+                --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
+            #else:
+                --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
+            #end if
+
           #end if
       #end if
 
@@ -123,9 +129,7 @@
                     <when value="rpkm" />
                     <when value="no" />
                     <when value="1x">
-                        <param name="normalizeTo1x" type="integer" value="2150570000"
-                            label="Report normalized coverage to 1x sequenceing depth"
-                            help ="Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
+                        <expand macro="effectiveGenomeSize" />
                     </when>
                 </conditional>
             </when>
@@ -203,13 +207,18 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
+You can find more details in the `bamCompare wiki`_.
+
+.. _bamCompare wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
+
+
 **Output files**:
 
 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.
 
 -----
 
-.. class:: infomark
+@REFERENCES@
 
     </help>
 </tool>
diff -r ea2f64efe70d -r 2f7edf06a5da bamCorrelate.xml
--- a/bamCorrelate.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/bamCorrelate.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -150,18 +150,19 @@
    :alt: Heatmap of RNA Polymerase II ChIP-seq
 
 
+You can find more details in the `bamCorrelate wiki`_.
+
+.. _bamCorrelate wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
+
+
 **Output files**:
 
 - diagnostic plot produced by bamCorrelate is a clustered heatmap displaying the values for each pair-wise correlation, see below for an example
 - data matrix (optional) in case you want to plot the correlation values using a different program, e.g. R, this matrix can be used
 
 
-
-
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>
diff -r ea2f64efe70d -r 2f7edf06a5da bamCoverage.xml
--- a/bamCoverage.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/bamCoverage.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -22,7 +22,11 @@
         #if $scaling.type=='rpkm':
             --normalizeUsingRPKM
         #elif $scaling.type=='1x':
-            --normalizeTo1x $scaling.normalizeTo1x
+            #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+                --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
+            #else:
+                --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
+            #end if
         #elif $scaling.type=='own':
             --scaleFactor $scaling.scaleFactor
         #end if
@@ -71,9 +75,7 @@
             <when value="rpkm"/>
             <when value="no"/>
             <when value="1x">
-                <param name="normalizeTo1x" type="integer" value="2150570000"
-                    label="Genome size"
-                    help ="Enter the genome size to normalize the reads counts. Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
+                <expand macro="effectiveGenomeSize" />
             </when>
             <when value="own">
                 <param name="scaleFactor" type="float" value="1" size="3" 
@@ -141,14 +143,17 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
+You can find more details in the `bamCoverage wiki`_.
+
+.. _bamCoverage wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
+
+
 **Output files**:
 
 - coverage file either in bigWig or bedGraph format
 
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>
diff -r ea2f64efe70d -r 2f7edf06a5da bamFingerprint.xml
--- a/bamFingerprint.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/bamFingerprint.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -134,6 +134,11 @@
 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
 
 
+You can find more details in the `bamFingerprint wiki`_.
+
+.. _bamFingerprint wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
+
+
 **Output files**:
 
 - Diagnostic plot
@@ -141,8 +146,6 @@
 
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>
diff -r ea2f64efe70d -r 2f7edf06a5da bigwigCompare.xml
--- a/bigwigCompare.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/bigwigCompare.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -94,10 +94,9 @@
 finally a summarizing value is reported. This value can be the ratio of the
 number of reads per bin, the log2 of the ratio, the sum or the difference.
 
+
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>
diff -r ea2f64efe70d -r 2f7edf06a5da computeGCBias.xml
--- a/computeGCBias.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/computeGCBias.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -132,6 +132,11 @@
 .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png
 
 
+You can find more details in the `computeGCBias wiki`_.
+
+.. _computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias
+
+
 **Output files**:
 
 - Diagnostic plot
@@ -146,8 +151,6 @@
 
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>
diff -r ea2f64efe70d -r 2f7edf06a5da computeMatrix.xml
--- a/computeMatrix.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/computeMatrix.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -208,9 +208,12 @@
    :alt: Relationship between computeMatrix, heatmapper and profiler
 
 
------
+You can find more details in the `computeMarix wiki`_.
 
-.. class:: infomark
+.. _computeMatrix wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
+
+
+-----
 
 @REFERENCES@
 
diff -r ea2f64efe70d -r 2f7edf06a5da correctGCBias.xml
--- a/correctGCBias.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/correctGCBias.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -90,14 +90,18 @@
 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.
 
+
+You can find more details in the `correctGCBias wiki`_.
+
+.. _correctGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
+
+
 **Output files**:
 
 - GC-normalized BAM file
 
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>
diff -r ea2f64efe70d -r 2f7edf06a5da deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/deepTools_macros.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -105,7 +105,9 @@
     </xml>
     <token name="@REFERENCES@">
 
-For more informations, please visit our `project site`_.
+.. class:: infomark
+
+For more informations, please visit the `project site`_.
 
 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
 
@@ -114,7 +116,7 @@
 
 .. _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
-.. _project site: https://github.com/fidelram/deepTools
+.. _project site: https://github.com/fidelram/deepTools/wiki/
 
     </token>
 
diff -r ea2f64efe70d -r 2f7edf06a5da heatmapper.xml
--- a/heatmapper.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/heatmapper.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -198,9 +198,12 @@
    :alt: Heatmap of RNA Polymerase II ChIP-seq
 
 
------
+You can find more details in the `heatmapper wiki`_.
 
-.. class:: infomark
+.. _heatmapper wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
+
+
+-----
 
 @REFERENCES@
 
diff -r ea2f64efe70d -r 2f7edf06a5da profiler.xml
--- a/profiler.xml	Fri Jan 31 05:12:41 2014 -0500
+++ b/profiler.xml	Sat Feb 01 06:04:58 2014 -0500
@@ -152,9 +152,12 @@
    :alt: Meta-gene profile of Rna Polymerase II
 
 
------
+You can find more details in the `profiler wiki`_.
 
-.. class:: infomark
+.. _profiler wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
+
+
+-----
 
 @REFERENCES@