# HG changeset patch
# User geert-vandeweyer
# Date 1392284756 18000
# Node ID 2799221681dda4ae00db3651d5551d4c2840141f
# Parent  39c374d4cba700b09719c34ee8da6f3b6b8a6380
Uploaded

diff -r 39c374d4cba7 -r 2799221681dd CoverageReport.xml
--- a/CoverageReport.xml	Thu Feb 13 04:45:48 2014 -0500
+++ b/CoverageReport.xml	Thu Feb 13 04:45:56 2014 -0500
@@ -1,5 +1,6 @@
-<tool id="CoverageReport" name="Panel Coverage Report" version="0.0.2">
+<tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.2">
   <description></description>
+  
   <command interpreter="perl">
     CoverageReport.pl
       ## input files
@@ -27,8 +28,9 @@
       #end if
   </command>
   <requirements>
-    <requirement type="package">BEDTools</requirement>
-    <requirement type="package">samtools</requirement>
+    <requirement type="package" version="2.11.0">R</requirement>
+    <requirement type="package" version="2.18.2">bedtools</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
     <requirement type="binary">pdflatex</requirement>
   </requirements>
   <inputs>
@@ -80,7 +82,7 @@
   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|Exon_number" : This is split on the 'Pipe' after 'GeneName' for correct grouping.
+  Column 4: Target Name. Use : "GENE-NAME&lt;space&gt;Exon_number" : This is split on the space after 'GeneName' for correct grouping.
   Column 5: Score : ignored, use '0'
   Column 6: Strand: ignored,'+' or '-'
 
@@ -111,14 +113,6 @@
   - Position in target region
   - Coverage at position
 
-------
-
-**Requirements**
-
-	- BEDTools (from toolshed)
-	- Samtools (from toolshed)
-	- pdflatex : binary must be in path, to create the pdf report.
-
   </help>
 </tool>