# HG changeset patch
# User geert-vandeweyer
# Date 1415262957 18000
# Node ID 6c7b09220992c5229260820f2d59af61ca5a6716
# Parent  43427b07e6bb0f7c86beda79515148f2d74f1b62
new version 0.0.3 (fix on headless R)

diff -r 43427b07e6bb -r 6c7b09220992 CoverageReport.xml
--- a/CoverageReport.xml	Wed Jun 18 08:18:10 2014 -0400
+++ b/CoverageReport.xml	Thu Nov 06 03:35:57 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.2">
+<tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.3">
   <description></description>
   
   <command interpreter="perl">
@@ -81,7 +81,7 @@
   Column 1: Chromosome : Use the same syntax as the references used by Galaxy. Check your sam-headers for the correct format. ('chr1' vs '1')
   Column 2: Start Position
   Column 3: End Position
-  Column 4: Target Name. Use : "GENE-NAME&lt;space&gt;Exon_number" : This is split on the space after 'GeneName' for correct grouping.
+  Column 4: Target Name. Use : "GENE-NAME|Exon_number" : This is split on the pipe (or space) after 'GeneName' for correct grouping.Example: "CLIP2|Exon_4"
   Column 5: Score : ignored, use '0'
   Column 6: Strand: ignored,'+' or '-'
 
diff -r 43427b07e6bb -r 6c7b09220992 readme.rst
--- a/readme.rst	Wed Jun 18 08:18:10 2014 -0400
+++ b/readme.rst	Thu Nov 06 03:35:57 2014 -0500
@@ -1,23 +1,18 @@
-Panel Resequencing Report
-=========================
-
-This wrapper was created by Geert Vandeweyer. It is free to use, adapt and redistribute, but  please mention the original source. 
+Panel Resequencing Report: This wrapper was created by Geert Vandeweyer. It is free to use, adapt and redistribute, but  please mention the original source.
 
-Installation
-============
 
-The recommended installation is by means of the toolshed_.
+Installation: The recommended installation is by means of the toolshed_.
 
 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/coverage_report
 
-
 Samtools, bedtools and R should be installed automatically by galaxy if not yet available. 
 PdfLatex must be installed manually and added to the PATH.
 
 
-History
-=======
+History:
+
 0.0.1 - Initial release, no dependency handling
 0.0.2 - Updated release, following toolshed recommendations.
+0.0.3 - Upgraded to R 3.0.3 (support on headless machines). Update to the documentation(targets bed format).
 
 
diff -r 43427b07e6bb -r 6c7b09220992 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 18 08:18:10 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 06 03:35:57 2014 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="3.0.2">
-        <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bedtools" version="2.18.2">
 	<repository changeset_revision="35905f2ae9f4" name="package_bedtools_2_18_2" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" />