Mercurial > repos > bgruening > deeptools

changeset 37:2f7edf06a5da draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Sat, 01 Feb 2014 06:04:58 -0500
parents ea2f64efe70d
children 9afae9d021cd
files bamCompare.xml bamCorrelate.xml bamCoverage.xml bamFingerprint.xml bigwigCompare.xml computeGCBias.xml computeMatrix.xml correctGCBias.xml deepTools_macros.xml heatmapper.xml profiler.xml
diffstat 11 files changed, 66 insertions(+), 31 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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@
 
--- 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>
--- 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>
 
--- 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@
 
--- 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@