# HG changeset patch
# User bernhardlutz
# Date 1390252774 18000
# Node ID 4a25bb3a8c6921f59d45dea4d6f1ccc84130c785
# Parent  057169fb41c781032f9f482d3b20c59aff3be918
Uploaded

diff -r 057169fb41c7 -r 4a25bb3a8c69 cor.xml
--- a/cor.xml	Mon Jan 20 15:08:40 2014 -0500
+++ b/cor.xml	Mon Jan 20 16:19:34 2014 -0500
@@ -48,19 +48,19 @@
 
 - **Pearson's Correlation** reflects the degree of linear relationship between two variables. It ranges from +1 to -1. A correlation of +1 means that there is a perfect positive linear relationship between variables. The formula for Pearson's correlation is:
 
-    .. image:: ${static_path}/images/pearson.png
+    .. image:: $PATH_TO_IMAGES/pearson.png
 
     where n is the number of items
 
 - **Kendall's rank correlation** is used to measure the degree of correspondence between two rankings and assessing the significance of this correspondence. The formula for Kendall's rank correlation is:
 
-    .. image:: ${static_path}/images/kendall.png
+    .. image:: $PATH_TO_IMAGES/kendall.png
 
     where n is the number of items, and P is the sum.
 
 - **Spearman's rank correlation** assesses how well an arbitrary monotonic function could describe the relationship between two variables, without making any assumptions about the frequency distribution of the variables. The formula for Spearman's rank correlation is
 
-    .. image:: ${static_path}/images/spearman.png
+    .. image:: $PATH_TO_IMAGES/spearman.png
 
     where D is the difference between the ranks of corresponding values of X and Y, and N is the number of pairs of values.
 
diff -r 057169fb41c7 -r 4a25bb3a8c69 histogram.xml
--- a/histogram.xml	Mon Jan 20 15:08:40 2014 -0500
+++ b/histogram.xml	Mon Jan 20 16:19:34 2014 -0500
@@ -71,7 +71,7 @@
 
 - Create a histogram on column 2 of the above dataset. 
 
-.. image:: ${static_path}/images/histogram2.png
+.. image:: $PATH_TO_IMAGES/histogram2.png
 
 </help>
 </tool>
diff -r 057169fb41c7 -r 4a25bb3a8c69 scatterplot.xml
--- a/scatterplot.xml	Mon Jan 20 15:08:40 2014 -0500
+++ b/scatterplot.xml	Mon Jan 20 16:19:34 2014 -0500
@@ -64,7 +64,7 @@
 
 - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset.
 
-.. image:: ${static_path}/images/scatterplot.png
+.. image:: $PATH_TO_IMAGES/images/scatterplot.png
 
 </help>
 </tool>
diff -r 057169fb41c7 -r 4a25bb3a8c69 short_reads_figure_score.xml
--- a/short_reads_figure_score.xml	Mon Jan 20 15:08:40 2014 -0500
+++ b/short_reads_figure_score.xml	Mon Jan 20 16:19:34 2014 -0500
@@ -56,7 +56,7 @@
 
 Quality scores are summarized as boxplot (Roche 454 FLX data):
 
-.. image:: ${static_path}/images/short_reads_boxplot.png
+.. image:: $PATH_TO_IMAGES/short_reads_boxplot.png
 
 where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines:
 
diff -r 057169fb41c7 -r 4a25bb3a8c69 static/images/histogram2.png
Binary file static/images/histogram2.png has changed
diff -r 057169fb41c7 -r 4a25bb3a8c69 static/images/kendall.png
Binary file static/images/kendall.png has changed
diff -r 057169fb41c7 -r 4a25bb3a8c69 static/images/pearson.png
Binary file static/images/pearson.png has changed
diff -r 057169fb41c7 -r 4a25bb3a8c69 static/images/scatterplot.png
Binary file static/images/scatterplot.png has changed
diff -r 057169fb41c7 -r 4a25bb3a8c69 static/images/spearman.png
Binary file static/images/spearman.png has changed
diff -r 057169fb41c7 -r 4a25bb3a8c69 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jan 20 15:08:40 2014 -0500
+++ b/tool_dependencies.xml	Mon Jan 20 16:19:34 2014 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="0a395bcd7efd" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="7c6ec22e9ef0" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="rpy2_2_3_6" version="2.3.6">
         <repository changeset_revision="ef3a897cf4f2" name="package_rpy2_2_3_6" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />