# HG changeset patch
# User yhoogstrate
# Date 1400675225 14400
# Node ID 31279ea9fbfaac3d8b8aade180dbc163d18f3b67
# Parent  84fd5f7ec18fe6aa9693126b3b413b58b39c9ad2
Uploaded

diff -r 84fd5f7ec18f -r 31279ea9fbfa featurecounts.xml
--- a/featurecounts.xml	Wed May 21 08:10:03 2014 -0400
+++ b/featurecounts.xml	Wed May 21 08:27:05 2014 -0400
@@ -194,59 +194,61 @@
 	</outputs>
 	
 	<help>
-featureCounts::
-**Overview**
-
-FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files.
-It has a variety of advanced parameters but its major strength is its outstanding performance: analysis of a 10GB BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome)!
-Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, Advance Access, accepted on Nov 7, 2013
+featureCounts
+#############
 
-featureCounts is part of a bigger analysis suite called subread:
-http://subread.sourceforge.net/
-Liao Y, Smyth GK and Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108, 2013
+Overview
+--------
+FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files.
+It has a variety of advanced parameters but its major strength is its outstanding performance: analysis of a 10GB SE BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome) [1].
 
-**Input formats**
-
+Input formats
+-------------
 Alignments should be provided in either:
-* SAM format - hhttp://samtools.sourceforge.net/samtools.shtml#5
-* BAM format
+
+- SAM format, http://samtools.sourceforge.net/samtools.shtml#5
+- BAM format
 
 Gene regions should be provided in the GFF/GTF format:
-* http://genome.ucsc.edu/FAQ/FAQformat.html#format3
-* http://www.ensembl.org/info/website/upload/gff.html
 
-**Installation**
+- http://genome.ucsc.edu/FAQ/FAQformat.html#format3
+- http://www.ensembl.org/info/website/upload/gff.html
 
-1) Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history.
+Installation
+------------
 
-2) Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml.
-https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables
+1. Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history.
 
-**Examples**
+2. Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml. More info at:  https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables
 
-**References**
+References
+----------
 
-featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
+**featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.**
 
-Liao Y1, Smyth GK, Shi W.::
+*Liao Y1, Smyth GK, Shi W.* Bioinformatics. 2014 Apr 1;30(7):923-30.
 
-* http://www.ncbi.nlm.nih.gov/pubmed/24227677
-* http://dx.doi.org/10.1093/bioinformatics/btt656
+- http://www.ncbi.nlm.nih.gov/pubmed/24227677
+- http://dx.doi.org/10.1093/bioinformatics/btt656
 
 
-**License**
+License
+-------
+
+featureCounts / subread package:
 
-* featureCounts / subread: GNU General Public License version 3.0 (GPLv3)
+- GNU General Public License version 3.0 (GPLv3)
 
-**Contact**
+Contact
+-------
 
 The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
-I want to thank the Marius van den Beek for his contribution as well.
+I want to thank the Marius van den Beek for his contribution to this wrapper.
 
 More tools by the Translational Research IT (TraIT) project can be found in the following repository:
-http://toolshed.dtls.nl/
+http://testtoolshed.g2.bx.psu.edu/
 
 </help>
 </tool>
\ No newline at end of file